The short answer
Late lodgements, payroll inconsistencies, and superannuation reporting issues can trigger ATO reviews or audits.
The bookkeeping issues most likely to attract ATO attention are late lodgements, big unexplained swings in income or GST, and payroll or super figures that don’t line up. The ATO now receives payroll data every pay run through Single Touch Payroll, so if super is reported but not paid, or wages don’t match your BAS, it shows up quickly.
Why do late lodgements matter so much?
Lodging BAS, tax returns or payroll reports late, again and again, is one of the clearest red flags. It can lead to failure-to-lodge penalties, interest on unpaid amounts and closer scrutiny of your business. Even if you can’t pay in full, lodging on time and arranging a payment plan is far better than not lodging.
What kinds of numbers trigger checks?
The ATO compares your figures with your history and with similar businesses. Large or unexplained changes can prompt questions:
Income or GST that drops sharply without a clear reason
GST refunds that are unusually large or frequent
Expenses well above industry benchmarks
Wages in payroll reports that don’t match wages on your BAS
How does Single Touch Payroll change things?
With STP, every pay run reports wages, tax withheld and super to the ATO. If super is reported but not paid to employees’ funds, the ATO can see the gap. From 1 July 2026, Payday Super requires super to be paid at the same time as wages, so the timing has to line up too.
Which other systems are connected?
Payroll data now flows across more systems, including payroll tax and WorkCover in many states. Inconsistent figures across these reports make a review more likely.
A typical Melbourne scenario
A café in Fitzroy fell three BAS periods behind during a busy year and paid staff super late. STP showed super reported but not paid, and the overdue BAS triggered reminder letters, then penalties. A bookkeeper caught up the lodgements, set up a payment plan for the backlog and scheduled super with every pay run. The ATO letters stopped within two quarters.
How do you stay off the radar?
Lodge every BAS and payroll report on time, even if you can’t pay in full.
Reconcile your accounts monthly so figures are accurate.
Make sure wages on payroll reports match your BAS.
Pay super with every pay run.
Keep receipts and explanations for large or unusual transactions.
Key takeaways
Repeated late lodgement is a major red flag.
Big unexplained swings in income, GST or expenses prompt checks.
STP lets the ATO match payroll and super in real time.
Accurate, on-time bookkeeping is the best protection.
General information only. Talk to your accountant or bookkeeper about your circumstances.
Read what happens when BAS is lodged late and how small errors become big compliance problems, or see our small business bookkeeping, payroll services and tax compliance services.
Marissa has over eight years of bookkeeping experience and a genuine passion for helping businesses take control of their finances. She's proactive, precise, and committed to making bookkeeping easy, accurate, and stress-free for every client she works with. Whether it's reconciling accounts, tracking cash flow, or streamlining financial systems, she's across the detail so you don't have to be.
