How the ATO checks super compliance¶

Super is far more visible to the ATO than it used to be. When you run payroll, you report each employee's pay and super to the ATO. Super funds also report what they receive. The ATO puts those two pictures side by side, so a gap between what was reported and what was actually paid is easy for them to see.

In one line

The ATO compares what you report through payroll against what super funds actually receive — so paying the right super on time is the simplest protection.

Why this matters¶

You do not have to do anything special for the ATO to notice unpaid or late super. The data comes to them automatically. Once you understand how the checks work, the best response is clear: pay the correct super to the fund on time, every time.

What you will learn¶

How the ATO matches payroll reports against super fund data
The role employee reports play
Why paying on time is your simplest protection

Understanding the concept¶

Every time you run payroll, you report each employee's pay and their super to the ATO through Single Touch Payroll (STP). Super funds separately tell the ATO how much super they have received for each person. The ATO explains that it matches these two sets of information for each employee, building one combined view of the super each person was owed and the super their fund actually received.

When those two numbers do not line up — for example, super was reported but never reached the fund, or reached it late — that shows up as a gap. The ATO uses this to spot super that was not paid, underpaid, or paid late.

The ATO also acts on employee reports. An employee who thinks their super is missing can report it to the ATO, and that report can prompt the ATO to look at your records.

If the ATO sees a gap, it may contact you. The ATO says that if you receive a letter or email and you believe you paid in full and on time, you should review your records and fix any data issues so your reporting matches what the fund received.

For accountants & bookkeepers

The ATO has invested in matching STP data against super fund contribution data at scale to identify non-payment, underpayment and late payment earlier. The ATO notes that mismatches can also come from data problems — for example a mismatched ABN or incomplete fund details — so clean, consistent reporting between payroll and the fund reduces the chance of a false gap being flagged.

Example¶

Nina runs a small cafe and pays super for her three staff. One quarter, a payment to a fund does not go through, but her payroll still reported that super was owed. The ATO sees the amount she reported through payroll, sees that the fund received nothing, and contacts Nina about the difference. Because the super had genuinely not reached the fund, Nina arranges to pay it and puts a reminder in place so it does not happen again.

Common mistakes¶

Assuming late or missed super will go unnoticed — the ATO sees both sides.
Treating "reported through payroll" as the same as "paid to the fund" — only money the fund actually receives counts.
Ignoring a contact letter instead of reviewing records and fixing data issues.

How this works in myaccountant¶

In the app — myaccountant keeps a record of the super worked out, reported and paid for each employee. If the ATO ever queries a gap, you can see what was owed and what was sent, so you can respond quickly and correct any mismatch.

Key points¶

The ATO matches your payroll reports against what super funds actually receive.
A gap between reported and received super is easy for the ATO to see.
The ATO also acts on employee reports of unpaid super.
If the ATO spots a gap, it may contact you to review and fix your records.
Paying the correct super to the fund on time is the simplest protection.

Learn next¶

General information only — not tax, super or financial advice.

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