Unexpected BAS refund? Check the figures before lodging

Run these checks while the business activity statement (BAS) is still a draft. If you have already lodged it, preserve that version and have the agent check the appropriate correction process before changing the underlying records.

Identify which refund the report is showing

For the GST component, 1A is GST on sales and 1B is GST on purchases. If 1B exceeds 1A, that component is a credit. The whole BAS can also include other obligations, and the ATO account may contain other balances. A GST credit in a worksheet isn't necessarily the final amount paid into your bank account.

Read the actual statement and its labels using the ATO BAS instructions. The BAS foundation guide explains the surrounding obligations. Record the reporting period, basis and draft run date before comparing it with anything else.

Compare the changes, not just the bottom line

Use the previous quarter and, where seasonal trading matters, the corresponding quarter last year. Compare sales GST, purchase credits and major one-off items separately. A refund caused by a large equipment purchase has a different explanation from a refund caused by falling sales.

Possible cause	Report to inspect	Evidence that resolves it
Major asset purchase	Largest GST purchase entries and asset register	Supplier tax invoice, business use, payment and attribution
Duplicate credit	GST purchase detail sorted by supplier and amount	One invoice linked to one claim; inspect bank-created duplicates
Negative sales	Credit notes and negative invoice lines	Original sale, agreed change and adjustment documentation
Wrong reporting period or basis	BAS settings and saved earlier reports	ATO registration settings and consistent period boundaries
Changed historical transactions	Audit log and prior-period adjustment report	Original lodged figures, changed entry and approved correction route
Import GST twice	Customs entries and freight-agent bills	One declaration amount matched across documents

Use the table as an investigation list. A matching explanation still needs its supporting documents. Original ASBG worksheet; all example figures are fictional.

Reconcile a fictional refund from $2,500 to $1,000

Assume a GST-registered business has $2,500 of sales GST and $5,000 of purchase credits in its draft. The reported GST component is $2,500 - $5,000 = negative $2,500, a $2,500 credit.

The review finds that a $16,500 machine invoice, including $1,500 GST, was entered twice: once as a bill and once from the bank payment. The machine is assumed fully creditable, with a valid invoice and correct timing. Only one $1,500 credit should be included.

Step	1A sales GST	1B purchase credits	GST outcome
Original draft	$2,500	$5,000	$2,500 credit
Remove duplicate purchase credit	$2,500	$3,500	$1,000 credit
Explain supported $3,500 credits	Unchanged	$1,500 machine + $2,000 other eligible purchases	Supported GST component: $1,000 credit

The duplicate correction occurs before lodgement in this example. No PAYG obligations, other BAS labels or ATO account offsets are included. Original ASBG worksheet; all example figures are fictional.

The remaining refund is plausible because of the machine purchase. That doesn't prove every asset purchase qualifies for a full GST credit. Private use, documentation, attribution and specific limitations still need checking under the ATO credit rules. An income-tax instant asset write-off is a different question from a GST purchase credit.

Check what changed after the last BAS

Accounting software can identify transactions added, edited or deleted after an earlier period was completed. MYOB's BAS guidance describes displaying prior-period changes. Review each change against the tax correction rules; the presence of a software adjustment does not determine the lawful reporting period.

Also check whether a GST code or report filter changed across many transactions. A new default code can create a consistent-looking error. If sales appear unexpectedly low, compare the invoice list, bank reconciliation and management revenue before accepting the refund.

Save the explanation before lodging

Prepare a short review note with the original draft result, identified differences, corrected result and unresolved items. Attach the invoices, adjustments, import declarations and relevant reports. Have the reviewer sign off the treatment, not just confirm the arithmetic.

After lodgement, retain the submitted BAS and receipt separately from the editable software report. Check the resulting ATO account position before counting on a payment date. The online lodgement guide covers the access and submission steps.

Continue with the next question

• Why BAS sales do not match your profit and loss report
• Reconcile your GST control account to lodged BAS amounts

Key takeaways

• Distinguish the GST component from the whole BAS and ATO account.
• Trace large changes to documents and remove duplicate claims.
• Save a supported variance explanation before submitting the return.

Where to get help

Ask a registered tax or BAS agent to review the unusual result and unresolved transactions. The Bookkeeping and BAS hub links the underlying records and reconciliation guides.