If you had any employees being paid on the number of units or per head or on total hours through taxable allowances that imply you have set up your employees on allowances and the setup seem to have not been done right. The gross amount comes up on the payslip but when you report to the ATO their tax shows up on the STP Portal but their gross wage shows up as zero.
- Find the employee it is showing incorrectly for.
- Go to employee record by clicking on the Employee >Edit employee.
- Find out which allowance the employee is on by clicking on Payments>Allowance.
- Go to Setup>Allowances> click on the allowance that the employee is on> Edit> click on the ATO payment Summaries tab. Untick the boxes as below and close to save it.
- Do STP update to update changes. Ensure the totals are correct.
If you had those boxes ticked for the taxable allowances then it shows separately on the payment summary considering it as a true allowance just like meal/telephone/rent allowance rather than a taxable allowance/wages. Anything that gets recorded in the payslip gets reported through STP Portal as part of wages. The system considers it as an actual true allowance to be reported separately on the payment summaries when you tick these boxes of reporting to ATO as it is under the payment summaries section.
To Do An STP Update
Click on the STP button and select STP update.
Untick all employees and select this employee only > OK.
Double-check all the totals.
Click on the Report To ATO button on the top right-hand side of the screen.