STP in ATO portal, payroll activity and payroll register number are different

Question

Hi There,

I am in the process of finalising STP for the 2025/26 financial year and have encountered an issue where the figures in the ATO portal, Payroll Activity report, and Payroll Register report do not match.

In December 2025, I accidentally processed a payroll for two employees, with gross wages of approximately $10,205 each. The payroll was reported to the ATO via STP.

Shortly afterwards, the business owner advised that these employees should not have been paid, as they were not entitled to a payment for that period. The employees were never paid through the bank account.

As a result, the December payroll should effectively be $0 for both employees.

The current situation is:

* ATO STP reporting shows approximately $10,205 for each employee in December 2025.
* Payroll Activity report shows $0 for both employees in December 2025, which I believe is correct.
* Payroll Register report shows negative gross wages of approximately ($10,205) for each employee in December 2025.

Because of this discrepancy, the Payroll Activity, Payroll Register and STP figures do not reconcile, and I am unable to confidently finalise STP.

Could you please advise:

* Why the Payroll Register is showing negative amounts while Payroll Activity shows zero?
* How I can correct the Payroll Register balances so that they match Payroll Activity?
* What steps are required to ensure the STP figures reported to the ATO are correct before finalising the 2025/26 payroll year?
* Whether an adjustment pay, payroll balance adjustment, or another correction method is required in MYOB Business.

Thank you for your assistance.

AnnaPhan7 · Answer

Hi Princess,

Thank you for your explanation.

Unfortunate, I have already processed a pay run dated in the new financial year.

I am trying to connect to MYB team to help me with.

Thank you again for your wonderful help.

Kind regards,

Anna Phan

Princess_R · Answer

Hi @AnnaPhan7,

Thanks for explaining everything so clearly. Mistakes like this can happen from time to time.

The main thing to know is that Payroll Activity and Payroll Register get their figures from different places. Payroll Activity is based only on the payroll transactions, while Payroll Register pulls from the employee card pay history. So if Payroll Register is showing negative amounts while Payroll Activity shows zero, it usually means the pay history on the affected employee card has been changed.

Fixing this normally means manually correcting the employee’s pay history on their card, but this can only be done if you haven’t already recorded a pay with a payment date in the new financial year. If you have already processed a pay run dated in the new financial year, this will need to be looked at by our team, as they’re the ones who can check and correct card history figures.

Before finalising, the first thing you’ll need is for Payroll Activity and Payroll Register to match. Once they do, you can send an update event and wait for it to show as accepted so the correct YTD figures flow through to the ATO.

Cheers,

Princess