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CZapp(Initiate)Initiate
4 June 2026

We changed payroll systems and providers in March. For active employees their YTD balances were moved across to the new system, and they are now showing duplicate STP statements.


For employees terminated prior to the new system going live in March, they need to keep their STP file from the old system. It is only those employees who have been active in both systems receiving duplicates, and their full YTD is in the new system so (I hope) it should be a straightforward matter of removing the old STP files from the old provider for those impacted employees.


We have limited access to the old system (external provider, going through their own transition). I have been able to find our old and new BMS ID - is there a way to provide a list of the impact employees and the two BMS ID's to the ATO to get the old STP from the old BMS ID removed?


I have tried calling the number on the ATO notice for advice but after going through the options the ATO phone lines say "we cannot take your call" and hang up.

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YellowPotato(Taxicorn)Taxicorn
4 June 2026

@PayrollDeanne would have a better answer


I think the simple solution would be to finalise the STP on the old system and then something along the lines of, only carry over the leave balances for existing employees to the new system. Not uncommon for employees to have two STP reports from same employer when switching payroll software

CZapp(Initiate)Initiate
4 June 2026

Hi Yellow Potato,


Currently all leave and YTD balances for ongoing employees are in the new system. It means that for these employees they have one STP file from the old payroll system (Preceda) with YTD up to mid march, then another STP file from the new system for 1 July to YTD, effectively double reporting the 1 July-mid march pay data.


Given this is where we are at, and we only have two weeks until our last pay for this financial year, I would appreciate any advice on how to proceed.

PayrollDeanne(Taxicorn)Taxicorn
4 June 2026

G'day @CZapp ๐Ÿ‘‹


@YellowPotato was right ๐Ÿ™‚


This is a very typical scenario and was included in the ATO STP2 Employer Guidance to prevent this issue ๐Ÿค“


You can see from that guidance that you need to finalise the terminated employees you didn't bring onto your current payroll system. Having the old/new BMS Id is good but you also need their old/new Payroll Id.


Separate income statements are published for each unique combination of ABN/Branch/BMS Id/ Payroll Id.


Find out how your new product supports this type of correction.


Also, ensure that you will be able to meet the record-keeping obligations of both the FWO (7 years) and the ATO (5 years). There are lots of leave and pay requirements that use averages over years ๐Ÿ˜‰


Deanne

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Change of payroll provider/system - How to fix duplicate STP files for employees? | ATO Community