For Single Touch Payroll (STP) to properly finalize terminated employees, all terminations must be processed within a pay. Simply entering a Termination Date and Reason under an employee’s Dates tab is insufficient.
To address a finalization error that occurs after processing a termination in a pay sequence, please follow the steps outlined below to resolve the issue:
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Open a Manual Pay.
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Adjust the Payment Date to 30/06 of the relevant financial year. To do this, access the transaction view, select the sequence, navigate to the employee, and press CTRL + A.
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Add the Termination allowance.
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Verify there are no payments included in the pay. If any payments appear, override them by entering 0.00.
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Process the pay using the appropriate option in the menu.
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Close the pay.
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Refinalize the employee(s).
Further resolutions to this error can be found here