The ATO Now Pre-Fills W1 and W2 On Your BAS. Here's What That Quietly Changed

Last reviewed against current ATO guidance: 12 Aug 2026. Always confirm current thresholds, rates, and dates at ato.gov.au.

For years, preparing the PAYG withholding section of a BAS meant reading figures out of the payroll system and typing them into labels W1 and W2. If they were wrong, you generally had until an audit to find out.

That changed. The ATO now pre-fills those labels from Single Touch Payroll data, and its guidance on STP and activity statements describes the intent as enabling employers to "tell us once".

The convenience is real. The second-order effect is what practices should be thinking about.

What is actually pre-filled

Per the ATO's guidance on PAYG withholding pre-fill for activity statements:

• W1 — total gross salary or wages and other payments made in the PAYG withholding month or quarter.
• W2 — total amounts withheld from the payments shown at W1.

Both are pre-filled in ATO online services from what you reported through STP. You can inspect the underlying STP report list in ATO online services to see exactly which submissions make up the pre-filled figure.

W3 and W4 are not pre-filled. Those amounts fall outside STP reporting scope, so they still require manual completion. This is a common source of error for anyone who assumes the whole section now populates itself.

The critical limitation

One sentence in the ATO guidance carries most of the operational weight: the ATO can only pre-fill your activity statement with the information you send through your STP-enabled software.

The pre-fill is not an independent calculation of what the client should have withheld. It is a mirror of what was reported. Which means:

• If a pay run was never lodged through STP, the pre-fill is understated — and it looks perfectly plausible.
• If an allowance is mapped to the wrong category under STP Phase 2, gross is misstated and W1 is wrong in a way no arithmetic check will catch.
• If a correction was made in payroll but no update event was sent, the pre-fill still carries the original figure.

A pre-filled field creates an impression of authority. It is worth being clear internally that these numbers are a reflection of the client's reporting hygiene, not a verification of it.

Where the reconciliation now sits

Under the old process, the reconciliation was payroll to BAS. You proved the figures you were about to type matched the payroll reports.

Now there are three points that all have to agree:

1. The payroll ledger — what the client actually paid and withheld.
2. The STP submissions — what the software reported to the ATO.
3. The bank account — what actually left the business.

The pre-fill only tells you about (2). A practice that accepts the pre-fill without tying it back to (1) and (3) has stopped reconciling and started transcribing.

The three-way check that matters each quarter:

• Gross wages per the ledger = W1 per the pre-fill.
• PAYG withheld per the ledger = W2 per the pre-fill.
• Net wages per the ledger = wage payments clearing the bank account.

If the first two agree but the third does not, you have a payment problem. If the first two disagree, you have a reporting problem — and the ATO is holding the version you did not intend to send.

Why the bank leg gets skipped

In most practices the third check is the one that quietly falls away, because it is the expensive one. Payroll reports and STP submissions both live in the payroll system, a couple of clicks apart. The bank leg means going to a different data set, reconciling it, and identifying which of a month's transactions are wage payments — split across multiple runs, sometimes multiple accounts, occasionally with individual employee payments made outside the normal batch.

That is exactly the work that gets deferred when a quarter is busy. And it is the leg that catches the errors the other two cannot: a duplicated pay run, a wage payment made from the wrong account, a director drawing coded to wages, a net payment that does not agree with the payslip.

If the bank side of the client's file is reconciled and coded continuously, this check costs a few minutes. If reconciliation happens in a scramble the week the BAS is due, it does not really happen at all — and W1 gets accepted because it was already in the box.

This is the case we make for ReconLink: bank feeds current, transactions coded against rules the practice controls, so the wages leg is already reconciled when the BAS falls due rather than being the reason it is late. Our interest in that conclusion is obvious; the three-way check stands on its own regardless of tooling.

A practical quarter-end routine

1. Run the payroll activity report for the exact BAS period — not year to date.
2. Open the STP report list in ATO online services and confirm which submissions make up the pre-fill.
3. Compare gross and withheld between the two. Investigate any variance before touching the BAS.
4. Reconcile net wages to the bank. Every wage payment in the period, including off-cycle ones.
5. Complete W3 and W4 manually. They are not pre-filled.
6. Only then accept the pre-fill. If you have changed a figure away from the pre-filled amount, document why.

Frequently asked questions

Which BAS labels does the ATO pre-fill from STP? PAYG withholding labels W1 and W2 are pre-filled in ATO online services from information reported through STP-enabled software.

What are W1 and W2? W1 is the total gross salary or wages and other payments made in the PAYG withholding month or quarter. W2 is the total amount withheld from the payments shown at W1.

Are W3 and W4 pre-filled too? No. Amounts reported at W3 and W4 are out of scope for STP reporting, so they cannot be pre-filled and must still be completed manually.

Can I change a pre-filled figure? The pre-fill reflects what was reported through STP. If it disagrees with the underlying payroll ledger, the right response is to investigate the cause — usually an unlodged pay run, a missing update event, or a pay category mapped incorrectly — rather than simply overwriting the number.

Where can I see what makes up the pre-filled amount? The STP report list in ATO online services shows the reported W1 and W2 amounts that make up the pre-fill.

Does the pre-fill mean my client's PAYG is correct? No. The pre-fill mirrors what was reported, not what should have been withheld. An underlying error that was reported consistently will pre-fill consistently and still be wrong.

The short version

Pre-fill removed the typing, not the reconciliation. The number in the box is now the ATO's copy of your client's reporting — so if it disagrees with the ledger, the discrepancy already exists on the ATO's side of the conversation. Reconcile all three legs, and complete W3 and W4 yourself.