Late STP reports and the pre-fill¶

When you go to lodge your activity statement, the wages and tax boxes are often already filled in for you. That is the pre-fill. The ATO builds it from the payroll reports it has received from you by a cut-off date. If one of your pay runs was reported to the ATO after that cut-off, it may not be counted yet — so the pre-filled figure can be too low.

If you lodge without checking, you can end up telling the ATO less than you actually paid and withheld. This lesson explains why that happens and how to catch it.

In one line

The pre-fill only counts the payroll reports the ATO had by a cut-off, so a late-reported pay run can leave it short — always check the figure against your actual payroll before you lodge.

Why this matters¶

Labels W1 and W2 on your activity statement come straight from your payroll. W1 is the total wages and similar payments; W2 is the tax you withheld from them. The ATO says it uses the payroll amounts you report to pre-fill W1 and W2 for you.

But the pre-fill is only as complete as the reports the ATO has received. If your last pay of the quarter was sent in late, the pre-fill may be missing it. Lodge that lower figure and you have under-reported — which usually means a correction later. Knowing about the cut-off lets you spot a short pre-fill before it becomes a problem.

What you will learn¶

How the ATO builds the pre-filled W1 and W2 from the payroll reports it has received by a cut-off
When a late payroll report can leave the pre-fill too low
How to check and adjust the figure against your actual payroll before you lodge

Understanding the concept¶

Every time you finish a pay run, your payroll software reports it to the ATO. The ATO adds up the reports it has received and processed for the activity statement period and uses those totals to pre-fill W1 and W2.

The catch is timing. The ATO only counts reports that have arrived and been processed by a certain point. It tells you when that was: the ATO says it shows the date of the latest payroll report included in your pre-fill, so you can see how up to date the figure is. Anything reported after that date is not in the figure yet.

So if a pay run is reported late — after that cut-off — the pre-filled W1 and W2 can be short by the wages and tax from that pay run. The figure is not wrong on purpose; it simply has not caught up.

Two things help you here:

The ATO says the pre-fill keeps updating each time a new payroll report comes in for that period — right up until you save or lodge the statement.
A late report is not lost. It still updates the ATO's records. If it arrives after you have already lodged, you may need to go back and correct the statement to match your actual payroll.

The safe habit is simple: before you lodge, compare the pre-filled figure with what your own payroll says you paid and withheld for the period. If they do not match, the pre-fill may be waiting on a late report.

For accountants & bookkeepers

The pre-fill for W1 and W2 is drawn from processed STP reports with a payment date inside the activity statement period, up to a stated cut-off shown on the prepare and edit screens. A year-to-date-only update report does not carry W1 and W2 totals, so they are not reflected in the pre-fill — only pay reports and adjustments move those labels. If a report lands after you save but before you lodge, the ATO flags that new STP data is available next time you view the statement. Where a late or corrected report changes an already-lodged period, revise that statement or carry the correction forward within the ATO's limits. Always reconcile the pre-fill to the payroll register rather than trusting it blind.

Example¶

Priya runs a small cafe with three staff and lodges her BAS each quarter. She finishes her June pay runs, but the very last one — a fortnightly pay dated late June — only gets reported to the ATO a few days into July, after she was away.

When Priya opens her activity statement, the pre-filled W1 shows about $58,000 and W2 shows about $9,000. That looks a little low to her. She checks the note on the screen and sees the ATO has included reports up to a date that falls before her last June pay was reported.

Priya opens her own payroll for the quarter. It shows total wages of about $62,000 and tax withheld of about $9,600 — because it includes that final pay run. The gap is exactly the pay that was reported late.

Because she checked, Priya adjusts the figures to match her actual payroll before she lodges, so W1 and W2 are complete. Her late-reported pay run still updates the ATO's records in the background — but her statement already tells the ATO the right amount, so there is nothing to fix afterwards.

Common mistakes¶

Trusting the pre-fill as final without checking the date of the latest report it includes.
Lodging a short figure because the last pay of the period was reported late — that under-reports W1 and W2.
Assuming a late report is lost — it still updates the ATO's records, and may mean correcting a statement you already lodged.
Forgetting to compare the pre-fill against your own payroll totals for the period before lodging.

How this works in myaccountant¶

In the app — when you finish a pay run, myaccountant reports it to the ATO for you. When you prepare an activity statement, myaccountant re-checks the pre-filled W1 and W2 so that a pay run reported late is picked up, and shows you the payroll totals to compare against before you lodge.

Key points¶

The ATO builds pre-filled W1 and W2 from the payroll reports it has received by a cut-off.
A pay run reported after that cut-off can leave the pre-fill too low.
The ATO shows the date of the latest report included, so you can see how current it is.
Always compare the pre-fill with your own payroll totals before lodging.
A late report still updates the ATO's records, and may mean correcting a lodged statement.
Reporting on time keeps the pre-fill complete and saves later corrections.

Learn next¶

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

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