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  • Correcting mistakes and disputing decisions

    Find out how to amend or vary your R&D tax incentive claim or dispute a decision.

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    Varying your registration or claim

    Once you have lodged your registration or your claim for the R&D tax incentive, you may find that you need to:

    • vary your registration details with the Department of Industry, Science and Energy
    • amend or vary your claim with ATO
    • dispute a decision made by either us or AusIndustry.

    If you need to correct or vary your tax return because you made a mistake or omitted to mention something you later realise you should have mentioned, you can also amend your tax return (within certain time limits).

    If you want to dispute the law as we have applied it to your case or if you are dissatisfied with the amount of R&D tax offset we have allowed, you can object to your assessment (within certain time limits).

    For information about varying your registration details or disputing decisions made by AusIndustry, refer to the Research & Development Tax IncentiveExternal Link guidance on

    Amending your tax return

    'Amendment' is the term we use for a change made to an income tax assessment. If you want us to change your income tax assessment you need to request an amendment in writing.

    Amendments are part of the self-assessment system. That is, just as we accept your tax return information at face value, in most cases we do the same with the information you provide on your request for an amendment.

    If you need to complete a company tax return, refer to Research and development tax incentive schedule 2022.

    Time limits for making amendments

    There are time limits for making amendments to your tax return. This is generally 2 years for small businesses and 4 years for other taxpayers. To give you certainty about your tax affairs, in most circumstances the law does not allow amendments (initiated by us or by you) outside the time limit, but you may be able to lodge an objection instead.

    Special rules vary these time frames for certain decisions AusIndustry makes in relation to the R&D tax incentive. These special rules allow us to amend outside of the standard timeframes in relation to:

    • AusIndustry giving the Commissioner of Taxation a finding, within certain timeframes, about registration, activities outside Australia, or core technology
    • an internal review decision by AusIndustry (on behalf of Industry Innovation and Science Australia), by the Administrative Appeals Tribunal (AAT), or by a court on certain matters.

    How to amend your claim

    If you wish to amend your claim for the R&D tax incentive you will need to:

    • complete and lodge an amended R&D tax incentive schedule for the relevant year, showing the amended figures
    • write us a letter to go with the amended schedule, requesting the amendment and specifying the labels on the company tax return that need amending.

    You must then forward your amended R&D tax incentive schedule and letter requesting the amendment to:

    Australian Taxation Office
    PO Box 3004
    PENRITH  NSW  2740

    Objecting to our decisions

    The law gives you the right to object to some decisions we make about your tax affairs, including most tax assessments. If you are dissatisfied with the amount of R&D tax offset we have allowed you, you can object to a decision.

    You must lodge your objection in writing and within certain time frames. In some circumstances you can also lodge an appeal with the Administrative Appeals Tribunal (AAT) or Federal Court.

    Time limits for lodging objections vary depending on whether you are objecting to an original income tax assessment, an amended income tax assessment, or a nil income tax assessment:

    In most cases, the time limit is at least 60 days from when you receive the notice and, in the case of income tax assessments, it is 2 or 4 years after the lodgment date for the return (2 years for small businesses or 4 years for all other taxpayers). If the final lodgment day falls on a non-business day, your objection can be lodged on the next business day.

    Time limits for objecting to original income tax assessments

    For income tax assessments you have 2 or 4 years from the date the notice of assessment was given to you, depending on what type of taxpayer you are (2 years for small businesses or 4 years for all other taxpayers).

    Time limits for objecting to amended income tax assessments

    For amended income tax assessments you have until the later of either:

    • 60 days from the date the amended assessment was given to you
    • 4 years from the date the original assessment was given to you (or 2 years for small businesses).

    Nil income tax assessments

    A 'nil assessment' is an assessment ascertaining that there is either:

    • no taxable income
    • an amount of taxable income and no tax is payable.

    Generally you cannot object against a nil assessment unless you are seeking to increase your tax liability. However, for the 2014 and subsequent income years, you can object against the total of your tax offset refunds for a year of income under the normal objection provisions. For the 2013 income year, there is a special rule allowing you to object to a nil income tax assessment if the objection relates to the 43.5% refundable R&D tax offset.

    If you wish to dispute the amount of a non-refundable R&D tax offset to be carried forward (where you have a nil assessment), you have to wait until you have an assessment for the year in which any part of the non-refundable R&D tax offset carried forward is first applied.

    How to lodge an objection

    Your objection must be lodged in writing. You can either use the form we provide or write a letter. Either way, your objection must be lodged within the time limit. You can fax your objection to us, post it, hand deliver it to a shopfront, or have your tax agent lodge it online. There is no fee for lodging an objection.

    If you are dissatisfied with the outcome of your objection, you can seek an external review of the decision by lodging an appeal with the Administrative Appeals Tribunal (AAT) or Federal Court.

    How to lodge an appeal

    Tax laws specifically give you the right to go to the AAT or the Federal Court of Australia for a review of some of our actions or decisions about your tax affairs. Generally you have to lodge an objection and be dissatisfied with the outcome before you can seek an external review. Certain time limits apply.

    Effect of AusIndustry findings on claims

    Findings made by AusIndustry (on behalf of Industry Innovation and Science Australia) bind us in making and amending assessments. We must use our amendment powers to give effect to findings. We must also give effect to any decision made by AusIndustry on internal review, and any decision about a finding made by the Administrative Appeals Tribunal (AAT) or a court.

    If a finding removes entitlement to some or all of the R&D tax incentive you have already claimed, you should request a self-amendment to adjust for the amount that cannot be claimed.

    If you do not amend your claim, we will commence an audit to give effect to the finding. We will not commence an audit for 28 days to allow time for a self-amendment request to be made.

    We are required to give immediate effect to a finding. This is not deferred by your request for an internal review by AusIndustry, or any AAT or court action. You should self-amend once you receive the finding.

    Concerns about repaying an debt

    If you have concerns about repaying an R&D debt, you can phone us on 13 28 66 so we can assist. This assistance is also available to those experiencing debt concerns while the original finding is under an internal review by AusIndustry. We will consider assistance after you have requested a self-amendment.

    Last modified: 22 Nov 2022QC 70877