Heffron
  • Home
  • About Us
    • Our Story
    • Our Team
    • Join our Team
      • Careers at Heffron
      • Students & Graduates
  • Fund Administration
    • For Professionals
      • Accountants
      • Advisers
    • For Trustees / Fund Members
  • Actuarial Certificates
  • Education & Support
    • For Professionals
      • Events
        • Event overview
        • Register for an event
      • Courses
        • Course overview
        • Super Foundations short course
        • Super Extension short course
        • Super Specialist short course
        • Mini Courses
      • Technical Support
        • Technical Support overview
        • Help Desk
        • Knowledge Centre
        • Super Companion
      • Documents
        • Request a document
        • Super Toolkit (Guided self-serve)
    • For Trustees / Fund Members
      • Overview of Trustee services
        • Knowledge Centre
        • Trustee Webinars
        • Technical Support
        • Request a document
  • News & Insights
  • Contact
Quick Access


    Contact Us

    Subscribe to our newsletter

    Our Services


    Fund Administration

    Advisers
    • Pricing and inclusions
    • Transition process
    • Establish an SMSF now
    • Transition an SMSF now
    • Request a sales call
    • SMSF wind up service
    Accountants
    • Pricing and inclusions
    • Onboarding Process
    • Request a sales call
    • SMSF wind up service
    Trustees / Fund Members
    • Pricing and inclusions
    • Transition process
    • Establish your SMSF now
    • Transition your SMSF now
    • SMSF wind up service

    Actuarial Certificates

    Volume packages
    • Request a sales call
    • Request an act cert (form)

    Education & Support

    Events
    • See all our events
    • Register for an event
    Courses
    • See all our courses
    • View Super Foundations sample
    • View Super Extensions sample
    Technical Support
    • Download Help Desk pricing
    • Legacy Pensions and Reserves
    • Division 296
    Documents
    • Professionals – Request a Document
    • Trustees – Request a Document
    Login

    Heffron Administration

    MAESTRO

    Heffron IQ Portal

    Education Bites Super Companion Super Foundations Super Extensions Super Toolkit
    1. Home /
    2. Knowledge centre /
    3. What is an smsf audit

    What is an SMSF Audit, what do auditors check and what does it all mean?

    In Practice Managing an SMSF
    Meg Heffron Meg Heffron
    |
    Managing Director | Actuary with 30+ years’ experience in SMSFs and co-founder of Heffron
    Published: April 30, 2026 | Updated: May 6, 2026

    Each year, every SMSF needs to be looked over by an auditor. They do two things – check that the fund’s financial statements are accurate (the “financial audit”) and look for areas where the trustees might not have complied with the super rules (the “compliance audit”). They provide a report to confirm they’ve done these things and, if they find problems, they’ll issue what’s known as a “qualified” report. Certain problems (eg high risk areas) need to be reported to the ATO in what’s known as an “auditor contravention report” (or ACR).

    Jump to...

    Getting audited each year is compulsory – SMSFs can’t lodge their annual income tax return with the ATO until it’s been done.

    What a 'clean SMSF audit report' means for your SMSF 

    A clean audit report means the auditor didn’t find any material issues of concern.

    Very few trustees go out of their way to do the wrong thing when it comes to their SMSF and so most hope for a clean bill of health from their auditor. That’s definitely a good thing. But it’s worth understanding what that really means.

    It doesn’t mean the auditor examined every single aspect of your super fund. Your auditor is only looking for material issues. This means they may only look at a sample of your fund’s transactions. A lot of the skill of audit lies in knowing how to find the “right” sample that gives them the best chance of spotting a problem.

    There are also some things the auditor can’t easily check and so will rely on statements from you. You may have been asked to sign a “trustee representation letter” for your SMSF – this is essentially you making these statements to the auditor. For example, you’re not eligible to be the trustee of your SMSF if you’ve been convicted of certain criminal offences. The auditor will ask you to confirm you haven’t done these things.

    When it comes to the financial audit, the auditor isn’t checking all of the tax calculations – that’s your tax agent’s job. The auditor will look more closely if they think your SMSF’s tax is materially wrong but they largely leave the question of what’s tax deductible and what’s not to whoever is preparing your fund’s tax return.

    The auditor will do some work to verify that your fund actually owns all the assets appearing on your financial statements. That’s why you might be asked to prove the right name (ie the trustee of your SMSF) is on your fund’s bank account, your investment accounts and title deeds etc. The auditor will also take steps to check these assets really exists. With shares, property etc it’s not that difficult but other more unusual assets can be trickier. For example, does your fund really own that gold, artwork or crypto? You’ll often be asked for extra proof!

    The auditor will also want to make sure the fund’s assets are appropriately valued in the financial statements. Again, this is easy where the fund owns cash, shares, managed funds etc as values are readily available. But more questions will be asked in the case of property or investments in unlisted entities.

    What a 'qualified SMSF audit report' means for your SMSF 

    Audit reports are divided into two parts – helpfully named Part A (the financial audit) and Part B (the compliance audit).

    Sometimes your fund will receive a qualified Part A report simply because the auditor wants to highlight there are certain things they haven’t checked. For example, anyone who moves from one auditor to another will often find the auditor will issue a Part A qualification because they can’t check last year’s numbers to make sure the starting point for this year’s audit was right. They will rely on the fact that the previous auditor has done their job.

    Other times you’ll receive a Part A qualification because your fund holds investments via platforms or wrap accounts. In this case, the auditor can’t necessarily check what your fund owns because they have to rely on the systems of the wrap provider.

    Of course, a more serious Part A qualification would be your auditor stating they didn’t feel your financial statements were right at all. Perhaps they think you’ve materially misstated the value of your assets, or they have genuine concerns your fund doesn’t have legal title to the investments you think it owns.

    If you receive a Part A qualification, there is no need to panic. But it’s important:

    • you understand the reason for the qualification,
    • you make your own assessment of the continued appropriateness and recoverability of the fund’s investments, and
    • if the value placed on your fund’s investments was of concern, you take steps to get more reliable evidence for next year’s audit.

    SMSF audit 'Part B qualifications' and 'Auditor Contravention Reports'  

    Often it’s the Part B qualifications that are more concerning – that’s where the auditor is highlighting your fund has broken one of the super rules in some way. Sometimes, the ATO also needs to be told about the problem in an ACR. This might be because of the particular rule which was broken, the amount of money involved, or whether it’s happened before.

    No-one likes being told they’ve done the wrong thing but it’s important you:

    • understand what you did wrong,
    • take action to fix the problem if you haven’t already, and
    • make sure it doesn’t happen again.

    For example, one of the things super funds can’t do is let their bank accounts be overdrawn. If this happens to your fund, make sure you always have enough cash in your super fund’s bank account to cover regular transactions including fees, and if necessary, cancel any overdraft facility.

    In extreme cases, breaking the super rules can mean more tax for your fund. You can also be fined or even sent to jail. But the ATO is able to overlook breaches if they were due to an innocent mistake, they’ve been fixed and steps have been put in place to make sure they don’t happen again.

    What’s an SMSF audit 'management letter'? 

    Sometimes auditors find things they think you should fix but they’re not serious enough to report via a qualified audit report or an ACR. These are another thing to pay attention to – if you don’t fix it, you might see an ACR next time.

    Annual SMSF audits are a fact of life. And the role of the auditor is really to report back to the ATO so they can be confident people with SMSFs are following the law and deserving of their tax concessions. Don’t be surprised to be asked to prove things or give extra information – there will be a reason.

    You may also be interested...

    • What happens at the end of financial year?

     


    This article is for general information only. It does not constitute financial product advice and has been prepared without taking into account any individual's personal objectives, situation or needs. It is not intended to be a complete summary of the issues and should not be relied upon without seeking advice specific to your circumstances.

     

    Contact Us

    Speak to an
    SMSF Consultant

    1300 HEFFRON

    Make an
    enquiry

    Boost your knowledge

    Newsletter signup

    • Knowledge Centre
    • News & Insights
    • Contact
    • Careers
    Facebook
    Linkedin
    Twitter
    Heffron

    © 2025 Heffron Consulting Pty. Ltd. trading as Heffron.  |  ABN 88 084 734 261  |  AFSL 241739  |  All rights reserved.

    • CPD Policy
    • Privacy Policy
    • Privacy Collection Statement

    The information shown on this site is general information only, it does not constitute any recommendation or advice; it has been prepared without taking into account your personal objectives, financial situation or needs and you should consider its appropriateness with regard to these factors before acting on it. Any taxation position described is a general statement and should only be used as a guide. It does not constitute tax advice and is based on the tax and superannuation laws which applied at the time the information was prepared and our interpretation. Your individual situation may differ, the tax and superannuation laws may have changed and you should seek independent up to date professional tax advice. You should also consider obtaining personalised advice from an adviser holding an Australian Financial Services Licence before making any financial decisions in relation to the matters discussed.

    HeffronLogo_RGB_Sm
    ×