payroll stp and activity not matching

When the Accountant went to work on the BAS lodgement for the quarter the ATO prefill is missing a pay week. When I looked into it the stp for that day has zero amounts like an update, yet the payroll activity/history eg MYOBs figures have a normal pay week , payroll showing a normal pay week with usual amounts. I have already paid the super for the quarter.

How do I fix this?? I can not reverse a pay that is linked in a super payment. I can not do another pay for that week or other figures will be over in MYOB??

Only way I can think to fix it is to do a pay run for that week again, lodge it (STP) so it hits the ATO, then do a journal to reverse the extra amounts going into gross wages, tax etc so figures in reports etc match what they should be - is that too easy have I missed something - will the reports like super work or will they only show the new payroll not the journal??

Genreve_S
2 months ago
Hi M0nty,

I get why seeing some of those STP lines showing $0 looks pretty worrying, but in this case, it’s usually not a sign that anything’s wrong.

STP isn’t the best place to judge what the ATO actually has. When a pay is reported as an update event (often when it’s processed after the original pay date or you choose “report as an update”), STP will show $0 for that period, but it still sends the year‑to‑date totals through to the ATO.

What really matters is that these three match for the payroll year:

Payroll Activity

Payroll Register

STP YTD / YTD Verification report

If those reports all line up, the ATO already has the correct YTD figures. In that case, your accountant can just override the BAS prefill to match your MYOB reports, and if you like, you can also send a Send update event from STP reporting to refresh the YTD at the ATO.

If you do find that STP YTD is actually short, the fix is not to rerun the pay and then journal it back out (that will only mess up payroll/STP further). Instead, once any setup issues are fixed, just send a clean STP Update event so the ATO gets the correct YTD without touching the original pay (which is already tied to the super payment).

Regards,

Genreve

4 Replies

Genreve_S
MYOB Moderator
2 months ago
Hi M0nty,

I get why seeing some of those STP lines showing $0 looks pretty worrying, but in this case, it’s usually not a sign that anything’s wrong.

STP isn’t the best place to judge what the ATO actually has. When a pay is reported as an update event (often when it’s processed after the original pay date or you choose “report as an update”), STP will show $0 for that period, but it still sends the year‑to‑date totals through to the ATO.

What really matters is that these three match for the payroll year:

Payroll Activity

Payroll Register

STP YTD / YTD Verification report

If those reports all line up, the ATO already has the correct YTD figures. In that case, your accountant can just override the BAS prefill to match your MYOB reports, and if you like, you can also send a Send update event from STP reporting to refresh the YTD at the ATO.

If you do find that STP YTD is actually short, the fix is not to rerun the pay and then journal it back out (that will only mess up payroll/STP further). Instead, once any setup issues are fixed, just send a clean STP Update event so the ATO gets the correct YTD without touching the original pay (which is already tied to the super payment).

Regards,

Genreve
M0nty
Contributing Cover User
2 months ago
thanks. I did do an update event hoping that might fix issue. I think it has worked. At this stage reports seem to be aligning my end so hopefully it will continue to match until end of financial year.
L-Mac
Contributing Cover User
1 month ago
hoping i can jump in here - I have just determined that the ATO prefill for March is out - all my MYOB totals are correct tho. Tracked it back to a pay event I processed mid March re an apprentice and paying 2 weeks of wages in one unscheduled payrun, I didnt use Base Hourly - I used Base Salary thinking this was easiest to enter a one off total pay with no PAYGW and NO SGC due to his hours/week not incurring {AYGW and his age not incurring SGC. We recvd a notification from ATO saying that a payroll category wasnt assigned. I have been back into payroll and amended it now.. it was Base Salary.. which I wouldnt normally use.. I have processed 2 pays since then and everything okay. BUT IT turns out that the entry of Base Salary has not been acknowledged by that ATO prefill.. Have sent a couple of update events but the GROSS in prefill is still incorrect. I thought I could amend the amounts in prefill and so I did and "saved" that area in the BAS awaiting EOQ completion.. if this is the solution (as all my end has the correct amount of GROSS and PAYGW and SGC) can I just send that draft amended prefill? Will this then have the ATO STP figure correct?
Princess_R
MYOB Moderator
1 month ago
Hi L-Mac,

Sure thing, and thanks for all the info you’ve shared. What you’re seeing can pop up when there’s a reporting error – in your case it’s tied to the ATO reporting category. We’d usually suggest fixing the incorrect setting first, then sending an update event to refresh the YTD figures sent to the ATO.

Yes, you can absolutely send that amended saved draft, as long as your payroll activity, register, and YTD verification reports all line up. However, changes made in BAS won't fix the STP figures because those are driven by the pay events/update events you lodge. So it’s best to double-check your payroll reports before making any changes.

Cheers,
Princess