R&D Tax Incentive – Top 10 Triggers for ATO Compliance

What are the top 10 triggers for an ATO compliance review

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ATO Compliance for the R&D Tax Incentive

The Australian Taxation Office (ATO) is dedicated to maintaining the integrity and efficiency of the nation’s taxation system. One significant area under their investigation is the R&D tax incentive.

Why does the ATO care?

So, why does the ATO keep such a close eye on this?

Here’s why:

  • Supporting Real R&D Projects – The R&D tax break isn’t just about money. It’s there to help new and exciting ideas come to life. The ATO wants to make sure that companies are using it for real research, not just to save some cash.
  • Saving Government Money – The R&D reward costs the government a lot – 3.2 billions in 2023. The ATO needs to make sure that only companies doing the right thing get this money, so it’s not wasted
  • Earning the Public’s Trust – For programs like the R&D incentive to work, people need to believe they’re fair. By checking and making sure companies follow the rules, the ATO helps keep everyone’s trust in the system.
  • Stopping Cheats – If the ATO didn’t check, some companies might try to claim money they don’t deserve. By keeping an eye out, the ATO makes sure companies stay honest.

Top 10 Triggers an ATO Review for the R&D Tax Incentive

When companies claim the R&D tax incentive, it’s important they’re doing it the right way. The ATO is always on the lookout to ensure companies are genuine in their claims. They have some key things they often check, which can hint that a deeper look is needed.
Here are some situations that might make the ATO pay closer attention.
  1. High R&D Costs vs. Overall Spending – If a company says most of their spending is on R&D, it can look suspicious.
  2. Paying a Lot to Friendly Companies – If lots of R&D money is going to companies that are closely connected, the ATO will want to be sure it’s all above board.
  3. Always Having High R&D Intensity – If a company’s R&D spending is always much higher than other similar companies, it might get noticed.
  4. Changing Feedstock Numbers – If the Feedstock numbers change a lot from year to year, it could be a red flag.
  5. Changing Company Details Often – If the details about connected or similar companies change a lot, it can look fishy.
  6. Owing the ATO Money but Claiming High R&D – If a company owes money to the ATO but is still claiming lots of R&D, it might seem like they’re not managing their money properly.
  7. New products but no R&D? – If a company says they’re earning lots but not spending much on R&D, the ATO might wonder why.
  8. Having Past Issues with the ATO – Companies that have had problems before might get checked more often.
  9. Being Different from Other Similar Companies – If one company’s R&D claims are very different from other companies in the same industry, it can stand out.
  10. Significant R&D rebates – If a company is always asking for big refunds, it can raise questions.

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1. High R&D Costs vs. Overall Spending 

It’s common sense that businesses would have varying operational costs. However, when the proportion of R&D expenditure to total costs starts to appear skewed, it can ring alarm bells. Let’s dissect this scenario further.

How High is Too High?

The real question is: what constitutes an unusually high R&D expenditure? Here are a few angles to consider:

  • Percentage Proportions – As a hypothetical, if Company A has an overall operational cost of $1 million for the financial year and claims $800,000 of that as R&D expenditure, that’s an 80% proportion. Such a high percentage might appear unusual, especially if this pattern is consistent year after year without a corresponding rise in innovative output.
  • Industry Benchmarks – If the majority of companies in a specific sector, say the agriculture sector, typically report around 10-15% of their expenses as R&D, then a company in the same sector claiming 60% might be seen as an outlier.


XYZ Tech Solutions Pty Ltd is a growing software company. In the 2022-23 financial year, they reported:

  • Total Operational Costs: $2 million
  • R&D Expenditure: $1.5 million

This means their R&D costs are 75% of their total spending.

Now, while high R&D costs are expected in the tech sector, 75% is substantially above the industry average. Most software companies of a similar size and lifecycle stage might report R&D costs between 30% and 50% of their total costs.

So, for XYZ Tech Solutions, this could be seen as a potential flag for the ATO, prompting a review to verify the genuineness of the claimed expenses.

Likely Trigger Percentages

While it’s hard to pin down a one-size-fits-all figure, based on industry norms and historical data, the following might be viewed as potential triggers:

  • Tech Industry: Above 60% of total costs
  • Pharmaceuticals:Above 70% (given the high costs of drug research)
  • Manufacturing:Above 40%
  • Retail: Above 20%

It’s important to note that these are illustrative figures. Each company’s situation is unique, and what might be a red flag for one might be business-as-usual for another.

2. Paying Associates:

When companies engage in transactions, it’s expected they’ll sometimes work with entities they have close ties with. However, when substantial sums are directed towards these “friendly” or payments to associates companies for R&D activities, it can pique the interest of the authorities. Let’s delve into this topic in more detail.

When Friendships Raise Eyebrows

The main concern with sizable payments to related parties lies in the principle of ‘arm’s length’. Here’s what to consider:

  • Arm’s Length Principle: In the realm of tax and corporate governance, transactions between associated entities are expected to be conducted as if they were between independent entities. This ensures that pricing is fair and prevents potential profit shifting.
  • Questioning Authenticity: If a company is continually directing a high percentage of its R&D expenses to a sister company or a subsidiary, it might appear as though they’re doing so to inflate costs or divert funds, rather than for genuine R&D activities.


ABC Robotics Ltd is a firm specialising in industrial automation. They frequently collaborate with DEF Components Ltd, a company owned by the same parent entity. In the 2022-23 financial year, ABC Robotics reported:

  • Total R&D Expenditure: $4 million
  • Payments to DEF Components for R&D services: $3.2 million

This means ABC Robotics directed 80% of its R&D spending to its associated company.

Given the high proportion of R&D expenditure directed to DEF Components, the ATO might consider this unusual, especially if similar firms in the industry have diversified R&D spending across various suppliers. This could prompt a review to verify if the costs claimed genuinely relate to R&D activities and if they’re priced at an arm’s length.

Likely Trigger Ratios

Using industry insights and historical patterns, we can suggest potential thresholds that might trigger closer scrutiny:

  • Tech and Manufacturing: Above 60% of R&D costs to a single associated entity.
  • Healthcare and Pharmaceuticals: Above 70% (given that certain specialized research might be centralized).
  • Agriculture: Above 50%.
  • Retail and Services: Above 40%.

However, it’s essential to understand that these figures are illustrative. Each company’s circumstances are unique, and contextual factors play a significant role in determining what might be deemed as excessive.


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3. Always Having High R&D Intensity

The R&D intensity of a company represents the ratio of its R&D expenditure to its total expenditure. A consistently high R&D intensity, especially if it’s considerably above the industry norm, can draw the attention of the ATO. Let’s explore this concept further.

Understanding R&D Intensity

R&D intensity is essentially a measure that shows the priority and emphasis a company places on its research and development activities. A high R&D intensity indicates that a large proportion of a company’s resources is dedicated to innovation and development, relative to other activities.

Why High Intensity Might Raise Questions

While innovation-driven companies naturally have a high R&D intensity, it becomes a matter of interest to the ATO when the intensity seems disproportionately high for extended periods. Here are a few concerns:

  • Industry Benchmarks – Every industry has its norms. If a company’s R&D intensity is consistently higher than the majority of its peers, it might be seen as an outlier.
  • Sustainability Concerns:Maintaining an extremely high R&D intensity over several years without corresponding revenue growth might seem unsustainable. This can lead to questions about the genuine nature of the reported R&D expenses.
  • Diversification of Expenditure: Companies typically have diverse operational costs. A high R&D intensity could suggest other expenses aren’t being reported accurately.

Worked Example

GreenTech Innovations Pty Ltd is an agri-tech company in Australia. Over the past three years, their financials report the following:

  • 2021: Total Expenditure: $5 million; R&D Expenditure: $4 million (R&D Intensity: 80%)
  • 2022: Total Expenditure: $5.5 million; R&D Expenditure: $4.4 million (R&D Intensity: 80%)
  • 2023: Total Expenditure: $6 million; R&D Expenditure: $4.8 million (R&D Intensity: 80%)

Considering the agri-tech industry’s average R&D intensity in Australia is around 40%, GreenTech’s consistent 80% might be viewed as atypical. This could warrant a closer examination to ensure all expenses and activities align with the R&D tax incentive’s requirements.

What Companies Can Do

For companies with genuine high R&D intensities, it’s vital to maintain detailed documentation and evidence of their R&D activities. This not only supports their claims but also offers clarity should any inquiries arise. Proper consultancy and periodic reviews can further ensure that their R&D claims are in line with ATO expectations.


4. Changing Feedstock Numbers

The feedstock provisions in the R&D tax incentive scheme ensure that businesses don’t gain a double benefit by claiming the tax incentive for R&D activities and then profiting from the resulting product without due consideration. A fluctuation in feedstock adjustments, especially if it’s significant and recurrent, can stand out when assessing claims.

Delving into Feedstock Adjustments

Feedstock adjustments come into play when a company’s R&D activities result in goods or products (referred to as feedstock outputs). The costs associated with producing these goods from the raw materials or inputs (known as feedstock inputs) are essential in determining the total R&D tax incentive a company can claim.

If there’s revenue generated from the sale or use of these feedstock outputs, it’s compared against the R&D costs, and necessary adjustments are made to ensure no double benefits are realised.

Why Changing Numbers Might Be a Concern

Consistent alterations in feedstock numbers can raise some eyebrows for a few reasons:

  • Inconsistent Revenue Reporting: If there’s a fluctuation in the feedstock revenue total from year to year, it could indicate inconsistency in how the company is reporting revenue from R&D derived products.
  • Variation in R&D Expenditure: Sudden spikes or drops in expenditure related to feedstock inputs might suggest the company isn’t maintaining a consistent R&D focus, or there could be potential misreporting.
  • Comparative Industry Analysis: If a company’s feedstock adjustments are inconsistent with what’s typical for their industry, it might be perceived as a deviation from the norm.


ClearWater Tech Pty Ltd is a company developing purification techniques for water. The purified water, a feedstock output, is sold to various industries. Over three years, their reported numbers are:

  • 2021: Feedstock Input Expenditure: $1 million; Feedstock Revenue: $500,000
  • 2022: Feedstock Input Expenditure: $1.2 million; Feedstock Revenue: $1.5 million
  • 2023: Feedstock Input Expenditure: $2 million; Feedstock Revenue: $600,000

Such fluctuating numbers in consecutive years might raise questions regarding the genuine nature of the feedstock input costs and revenues.

Best Practices for Businesses

For businesses that have legitimate reasons for fluctuating feedstock numbers, thorough documentation is the key. It’s essential to have clear records detailing the reasons for significant changes in feedstock adjustments. This will support the company’s claims and provide clarity during any potential reviews. Regular consultations with experts in the R&D tax incentive scheme can also help ensure accurate and compliant reporting.

5. Changing Company Details Often

One of the factors that may raise concerns or draw attention from the ATO in the context of the R&D tax incentive scheme is frequent changes to a company’s details. It’s not uncommon for businesses to evolve and undergo changes, but when these shifts happen often and seem inconsistent, it can lead to scrutiny.

Understanding the Implications

Companies need to provide specific details when applying for the R&D tax incentive. This includes not just information about the R&D activities but also about the company itself, such as affiliated entities, ownership, and more.

Why Frequent Changes Might Be Red Flags

  • Ownership and Control:Changing details related to company ownership or control can impact the assessment of a company’s R&D tax incentive claim. Frequent changes might suggest attempts to manipulate the eligibility criteria or the quantum of the claim.
  • Affiliated or Connected Entities: If there’s a regular reshuffling of affiliated entities or a pattern of frequent changes to connected entities, it can lead to concerns about the transparency and authenticity of the R&D activities and expenditures reported.
  • Inconsistency in Reporting:Consistency is crucial for establishing credibility. Regular alterations in company details can lead to questions about the genuineness of the R&D claims.


SolarTech Innovations Pty Ltd is a company researching sustainable energy solutions. Over the span of three years, they undergo the following changes:

  • 2021: Changes in major shareholding entities.
  • 2022: Alteration of the registered address and connected entities.
  • 2023: Transformation in the company’s board of directors and addition of new affiliated entities.

Such continuous shifts, especially if they are not in line with business growth or restructuring reasons, can lead to additional scrutiny by the ATO.

Best Practices for Companies

While there are legitimate reasons for altering company details (e.g., business expansion, mergers, restructuring), it’s crucial to maintain transparency. Companies should:

  • Maintain Thorough Documentation: Any change in company details should be well-documented with clear reasons provided. This will be invaluable if the ATO requests an explanation.
  • Seek Expert Advice: Before making significant changes, it’s wise to consult with professionals who understand the R&D tax incentive landscape. They can provide guidance on the potential implications of these changes.
  • Be Proactive in Communication: If the company anticipates frequent changes due to specific business reasons, consider proactively informing the ATO or providing additional context in the R&D claim submission.

Remember, while change is a part of business growth, the key lies in ensuring these changes are genuine, transparent, and well-documented.


6. Owing the ATO Money but Claiming High R&D

When companies are deep in arrears with the ATO but simultaneously lodge significant R&D tax incentive claims, it can draw the ATO’s attention. There’s a perception risk here: on one hand, a company claims to be undertaking substantial R&D activities requiring significant funding, but on the other, it appears unable to meet its tax obligations.

Delving Deeper into the Concern

From the ATO’s perspective, there’s an inherent contradiction when a company claims large R&D refunds while owing substantial tax debts. Here’s why this situation can be problematic:

  • Financial Management Concerns:Large outstanding ATO debts may suggest potential issues with a company’s overall financial compliance or management. If a company cannot manage its tax liabilities, how can it adequately manage its R&D expenditures?
  • Authenticity of the Claim: The ATO might question the genuineness of a significant R&D claim, especially if other financial indicators (like outstanding tax liabilities) suggest financial stress or mismanagement.


BioTech Solutions Pty Ltd is a company working on cutting-edge medical research. In 2023, they submit an R&D tax incentive claim of $500,000. However, their outstanding ATO tax liabilities from previous years amount to $300,000. This disparity raises eyebrows at the ATO, prompting them to review the company’s R&D claim more closely, especially if this pattern repeats over multiple years.

What Companies Should Consider

For companies in this position, it’s essential to be aware of how this looks and to take proactive measures:

Clear Communication: If there are genuine reasons for the outstanding ATO debts and the high R&D claim, it’s essential to communicate this clearly. This might involve providing additional context or documentation with the R&D claim submission.
Address Outstanding Debts: Whenever possible, companies should aim to address or negotiate a payment plan for their outstanding tax liabilities. Demonstrating a commitment to meeting tax obligations can go a long way.
Engage Professional Help: Engaging a tax or R&D consultant can help in assessing the situation and providing guidance on how best to approach the R&D claim, especially when there are outstanding tax liabilities.

In summary, while owing money to the ATO doesn’t automatically invalidate a legitimate R&D claim, it’s essential for businesses to understand the optics of the situation and take measures to ensure their R&D claims are seen as credible and genuine.

7. Making Big Money but Claiming Little R&D

It may sound counterintuitive at first: a business generating substantial revenue but claiming a minimal amount for R&D. On the surface, it might seem like a positive, indicating that the company is efficient in its research processes. However, from a compliance perspective, such a scenario can draw the attention of the Australian Taxation Office (ATO). The ATO might wonder why a company with significant resources isn’t investing more in R&D or whether the reported R&D figures truly reflect the company’s activities.

Probing the Discrepancy

Understanding why such a situation might be flagged by the ATO involves delving into a few key considerations:

  • Under-Reporting Suspicions: One of the primary reasons for scrutiny is the potential suspicion that a company is under-reporting its R&D expenses, perhaps to minimise scrutiny or because of misunderstandings about what can be claimed.
  • R&D Intensity Norms: Industries typically have an average ‘R&D intensity’ – a ratio of R&D expenditure to revenue. Companies significantly deviating from this norm, especially on the lower end, might be seen as outliers.


FutureTech Industries Pty Ltd, a tech company, has revenues exceeding $20 million in 2023. Despite being in an industry where R&D is often a significant cost, they claim only $50,000 in R&D expenses. This is far below the industry norm, making the ATO curious. They might wonder if FutureTech is genuinely spending so little on R&D or if they are not adequately capturing all eligible R&D expenses.

Navigating the Situation

Companies finding themselves in this position can take several steps:

  • Thorough Documentation: Ensure that all R&D activities are meticulously documented. This not only aids in accurate reporting but also ensures that the company can substantiate its claims if questioned.
  • Review Eligible R&D Activities: It’s essential to periodically review what constitutes eligible R&D activities. Sometimes, companies might be engaging in R&D without realising some activities qualify for the incentive.
  • Industry Benchmarking: Understand the typical R&D intensity for the industry. If the company’s R&D claim is much lower, be prepared to explain the reasons behind this.
  • Engage Experts: Consider seeking advice from R&D tax consultants. They can provide insights into industry norms and ensure that the company isn’t inadvertently missing out on eligible claims.

While having high revenue and low R&D claims isn’t inherently problematic, it’s crucial for businesses to understand how such a scenario might be perceived and ensure they are claiming all entitled R&D incentives accurately.

8. Having Past Issues with the ATO

A company’s history with the Australian Taxation Office (ATO) can play a significant role in its present and future interactions with the agency. Specifically, if a company has previously encountered compliance issues or discrepancies with the ATO, it could be at a higher risk of scrutiny for its R&D tax incentive claims.

Why Prior Issues Matter

  • Trust and Credibility: Repeated non-compliance or errors in past submissions can erode the ATO’s trust in the company’s reporting. It can create a perception that the company either lacks the processes to accurately report or may be intentionally misrepresenting figures.
  • Patterns of Behaviour: The ATO uses past interactions to identify patterns. If a company has historically been found to misinterpret R&D tax incentive guidelines or has made erroneous claims, the ATO might anticipate similar issues in the future.


GreenTech Innovations Pty Ltd had issues three years ago where the ATO found discrepancies in their tax returns unrelated to R&D. Last year, they made a substantial R&D claim. Given their past, the ATO might decide to take a closer look to ensure everything is above board.

How to Navigate Past ATO Issues

  • Transparency is Key: If the company knows that a prior issue might raise concerns, being proactive and transparent about current claims can be beneficial. This might involve providing more detailed documentation or explanatory notes with submissions.
  • Seek Expertise: Engaging with R&D tax consultants or specialists can help ensure that current claims are accurate, eligible, and well-documented. Their expertise can be invaluable in navigating the complexities of the R&D tax incentive, especially if there’s a history of compliance issues.
  • Open Communication: If the ATO reaches out with questions or concerns, responding promptly, transparently, and cooperatively can help build credibility and trust.
  • Implement Robust Processes: Ensure that internal processes for tracking and documenting R&D activities and expenditures are robust. This not only aids in accurate reporting but also demonstrates to the ATO a commitment to compliance.
  • Regular Reviews: Periodically review R&D tax incentive claims, especially if there have been issues in the past. This can help catch potential errors or misinterpretations before they become problematic.

While past issues with the ATO can increase scrutiny, companies can take proactive steps to ensure they’re viewed as compliant and trustworthy in their future R&D tax incentive claims.

9. Being Different from Other Similar Companies

In the realm of R&D tax incentives, adhering closely to industry norms and standards often plays in a company’s favour. A claim that diverges significantly from what is typical among similar companies might draw the attention of the Australian Taxation Office (ATO). While being unique isn’t inherently a problem, it’s essential to be prepared to justify any unusual figures or patterns.

Understanding Industry Norms

Every industry has its own standard practices when it comes to R&D spending. For instance, biotech firms might naturally have higher R&D expenditures due to the nature of their work, whereas a retail business might have minimal R&D costs. The ATO is well-aware of these norms and uses them as a benchmark.

Reasons for Discrepancies

  • New Market Strategies: A company might be trying out innovative strategies that aren’t common in the industry yet. This could mean higher or lower R&D expenditure compared to peers.
  • Different Business Models: Not every company in an industry operates the same way. Some might outsource R&D, while others do it in-house, leading to different reporting figures.
  • Entering New Business Territories: Diversification into new areas might necessitate unique R&D efforts, causing a temporary spike or drop in R&D expenditure.


PureWater Pty Ltd, a company in the water purification industry, decides to explore a groundbreaking filtration technique. Most competitors continue using established methods. As a result, PureWater’s R&D expenditure for the year is significantly higher than industry counterparts. This divergence might catch the ATO’s attention.

Staying in the Clear

  • Detailed Documentation: Maintain clear records that outline why the company’s R&D activities or costs are different. This might include project proposals, market research, or strategic business plans.
  • Engage with Specialists: If aware that the company’s figures diverge from the norm, it might be beneficial to engage with R&D tax consultants. They can provide guidance on documenting and presenting the claims in a way that’s comprehensive and justifiable.
  • Transparent Reporting: If the company’s R&D claims are atypical, provide as much detail as possible when submitting to the ATO. This proactiveness can demonstrate the legitimacy of the claim.
  • Stay Updated on Industry Trends: Regularly review what competitors and the industry at large are doing. This can provide insights into how the company’s R&D activities compare and if any discrepancies might arise.

While standing out from the crowd can be a strength in business, it’s crucial to be prepared when it comes to R&D tax claims. Understanding industry norms, keeping detailed records, and being proactive in communication can ensure that being different doesn’t lead to unwarranted complications with the ATO.

10. Significant R&D Rebates

Receiving a substantial R&D tax incentive is an indication of a company’s commitment to research and development. However, if a business consistently records large recoupments year after year, it might draw the ATO’s attention. While such claims are not inherently problematic, understanding the nuances can help businesses navigate potential pitfalls.

How Significant is Too Significant?

The key is discerning what might be considered unusually high recoupment. Here’s how you can approach this:

  • Pattern Analysis: If Company Beta claims a vast sum for the R&D tax incentive every year without showing proportional advancements or growth in their R&D projects, it may raise eyebrows.
  • Comparison with Industry Counterparts: A company’s R&D claims might be viewed in the context of its industry peers. If most competitors in a sector claim an average of $500,000 as R&D incentives and one specific firm consistently claims $2 million, it may appear as an outlier.


GenTech Solutions Pty Ltd, a biotech startup, has been at the forefront of genetic research. Over the past three years, they’ve consistently lodged significant R&D tax incentive claims.


  • 2021-22 Financial Year R&D Claim: $2 million
  • 2022-23 Financial Year R&D Claim: $2.2 million
  • 2023-24 Financial Year R&D Claim: $2.5 million

For a biotech startup, high R&D costs are not unusual given the nature of their work. However, the consistent escalation in claims without a corresponding increase in research output or marketable products could be seen as a potential red flag by the ATO.

Probable Trigger Points

While there isn’t a fixed “trigger amount”, historical data and industry norms can give an insight into what might be viewed as excessive:

  • Tech Industry: Claims above $1.5 million annually without substantial IP creation.
  • Pharmaceuticals: Consistent claims above $3 million without progressing to clinical trials or patent registrations.
  • Manufacturing: Yearly claims above $1 million without evident product innovations or enhancements.

These figures are indicative, and businesses must understand their unique situation and ensure their claims align with genuine R&D activities.


Just to set the record straight: this guide has been prepared with thoroughness and diligence. However, it’s essential to understand it’s not an instruction manual to navigate around the ATO’s scrutiny. Trust me, their tech tools and expertise are top-notch. While we’ve tried to provide insights, the figures are rough estimates, and the examples are purely fictional.

Always engage with a professional for your specific situation. Here’s to informed decisions, clarity, and a touch of humour along the way! Remember, it’s always best to play by the rules and keep things transparent.

Your Trusted Partner in Navigating the R&D Tax Incentive Waters

Navigating the complexities of the R&D tax incentive can be daunting, and the fear of potential ATO compliance checks only adds to the challenge. But you don’t have to go it alone. This is where Bulletpoint steps in, shining a light on the intricate pathways of R&D claims.

  • A Decade of Expertise: With over ten years in the business, we’ve become synonymous with proficiency in the R&D tax incentive realm. Our extensive experience is a testament to our commitment and dedication to our clients.
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At Bulletpoint, we’re not just about numbers; we’re about partnerships. We believe in making the R&D tax incentive accessible, understandable, and, most importantly, beneficial for you. Our approach is personable and straightforward. No jargon, just clear, actionable insights tailored to your needs.

So, if you’re seeking an ally who can guide you, support you, and stand by you in the R&D tax incentive journey, look no further. Let’s make innovation rewarding together. Reach out to Bulletpoint today and give your R&D claims the expert touch they deserve.

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