MYOB payroll register and STP Finalisation report don't match prefilled figures in ATO BAS

Question

We finalised our 2024 FY payroll in early July and our payroll register figures matches the STP Finalisation report to the cent.  However, when we lodged our BAS for the Apr- Jun quarter this week, the numbers preloaded by the ATO for gross pays and PAYG did not match.  It looks like a pay reversal did not go through to the ATO, but it is reflected in our STP2 numbers from MYOB.  I remember completing an update event to ensure that the figures all matched, when running a final payroll in June - but clearly, something went wrong.  It is now late August and I have no idea how this could have happened or what to do to fix it.

Genreve_S · Answer

Hi @HoneySandra,

No worries, it’s pretty normal for the amounts on your STP to look a bit off if you’ve done a reversal for that period. Because the STP sees the reversal as an update, it can throw things out of whack.

Feel free to override those ATO prefilled amounts so they match up with the correct figures.

Regards
Genreve

HoneySandra · Answer

Hi

I have exactly the same problem.

I reversed a pay, then re-entered it correctly. All YTD MYOB STP amounts match to every employee perfectly, but the month I did the reversal (August), shows a discrepancy in the ATO Pre-fill report for IAS.

The amount that the ATO  is out by is exactly the difference between the 2 pays that were corrected.

Is it still appropriate then to override the ATO Pre-fill amounts and enter with the MYOB amounts?

Isaiah_C · Answer

Hi @caroleob,

I understand how concerning it can be when discrepancies arise between your MYOB records and the ATO's pre-filled figures, especially after you've taken the necessary steps to ensure accuracy.

You can delete the draft of your BAS and set it up again. When you recreate it, ensure that the linked payroll categories are set up correctly. This can help to pull in the correct figures from your MYOB data, including the updates you made.

Alternatively, you can manually adjust the figures in the relevant boxes on your BAS to reflect the correct gross pays and PAYG withholding amounts. This will allow you to lodge the BAS with the correct figures, despite the discrepancy.

Regards,

Sai