The GST calculation uses a different accounting method from the business

The two reports do not measure the same period

You believe a GST estimate is too high because the bank receipts for the quarter are lower than the sales report. Before treating the difference as an error, ask your tax adviser which GST accounting method applies. A bank total and an invoice-based report may include different transactions for timing reasons, even when both were extracted accurately.

Identify the settings and the underlying records

Provide the relevant BAS history, software report settings, invoices, receipts and credit records. Record the date range used for each report. Do not change the software method simply to produce a smaller number. Ask the adviser to confirm the method actually applicable to the business and period, including any properly made change that affects the comparison.

Use the ATO distinction carefully

The ATO explains that GST can be accounted for on a cash or non-cash basis and that the method affects when GST is reported. Have the adviser apply the relevant rules to the actual transactions. This article does not select a method, determine eligibility to change it or calculate the amount of a particular tax liability.

Source: ATO: Choosing a GST accounting method

Consider a hypothetical quarter-end invoice

Imagine a business issues an invoice near quarter end and receives payment later. One report follows invoice dates while another follows receipt dates. The apparent mismatch needs a timing reconciliation before it can support an explanation to the ATO. Whether and when the particular transaction belongs in the GST calculation should be confirmed by the registered adviser.

Explain the difference instead of hiding it

Prepare a bridge between the reports showing identified timing items and unresolved questions. Keep copies of the original exports with their settings. Do not overwrite old reports so they appear to have always used the revised basis. If transactions need correction, follow the adviser's instructions and preserve an audit trail of the reason and supporting evidence.

Keep the notice response on track

Ask what the estimate notice itself requires and who will complete the response. A report reconciliation does not automatically change the estimate or any associated legal document. The practical goal is a calculation prepared on the correct basis, with an explanation of timing differences that the adviser can review and use appropriately.