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Hi Roger,
The system is designed for employees that are being paid regularly moreso than larger lump sum payments paid intermittently, and so the PAYG amounts are calculated based on average earnings across the expected financial year. In order to assist with this, there is a function in payroll to process Lump Sum payments, and different methods for calculating the PAYG on these amounts - you can view the articles here and here for more information on how this is calculated in the system. Regardless, you may find that manually calculating the PAYG that you are expecting to pay and creating an adjustment to correct this amount might suit your needs better. In order to create a PAYG adjustment, follow the steps below:
Regarding the BAS/STP figures that have been recorded, you may wish to update an existing pay run or create a new ad-hoc pay run in order to adjust the earnings for the financial year before lodging, however I would recommend reaching out to our support team directly in order to go over this process in more detail if you have any questions about this process. You can give them a call on 1800 0496 038 and they'll be able to discuss your specific situation in more detail and ensure that the figures are updated accordingly.
-Lucas