Missed a BAS? What to do, what it costs and how to catch up
The 28th came and went, the statement is still sitting in ATO online services, and you are not sure whether the right move is to lodge quietly or brace for a penalty. Lodge. This guide explains what a missed BAS actually costs, how the ATO tends to treat a first lapse, and how to get back on track whether you have missed one quarter or six.
Updated 16 September 2026. General information only, not tax advice.
Step 1: lodge, today
Two separate things happen when a BAS is late: a penalty for not lodging, and interest on any amount you have not paid. Lodging fixes the first immediately. Lodging without paying is normal and the ATO’s own guidance is to do exactly that.
If you do not have the figures, do the best job you can from the bank statement for the period and lodge it. Upload the statement to FlowFi, check the categories, and the labels are there. A lodged BAS with a small later correction is far better than an unlodged one. See how to lodge your BAS online.
If you had no activity in the period, lodge a nil BAS. A registered business must lodge even with nothing to report.
What the penalty is
The failure-to-lodge penalty is worked out in penalty units. For a small business it is one unit for each 28-day period, or part of one, that the statement is overdue, up to a maximum of five units. The dollar value of a penalty unit is set by law and changes from time to time (it is a few hundred dollars), so check the ATO for the current figure. Medium and large businesses pay multiples of that.
In practice the ATO does not always apply it. Its stated approach is to warn first for isolated cases, and to remit penalties where a business has a good lodgement history and a reasonable explanation. If a penalty does land, you can ask for it to be remitted through online services or by phone; explain what happened and what you have done to fix it.
What the interest is
General interest charge (GIC) accrues daily on any unpaid tax debt from the due date, at a rate the ATO publishes each quarter. It compounds, so a debt left for a year grows noticeably. GIC used to be tax deductible; from 1 July 2025 it is not, which makes leaving a BAS debt unpaid more expensive than it once was. Check the ATO for the current rate and rules.
You can ask for GIC to be remitted, but it is granted less readily than the lodgement penalty and usually requires circumstances beyond your control.
Step 2: pay, or set up a payment plan
If you can pay, pay using the payment reference number on the statement; it clears the debt and stops GIC. If you cannot, set up a payment plan in ATO online services. Most small business debts can be arranged online without a phone call: you choose an upfront amount and a schedule, and as long as you keep to it and lodge everything else on time, the ATO leaves you alone. Interest continues on the outstanding balance.
Be realistic about the schedule. A plan you default on is worse than a longer plan you keep.
If you have missed several
Lodge them all, oldest first, so each period’s figures are right and any refunds offset later debts. Work quarter by quarter from bank statements; if your bank only offers a limited history online, ask for older statements or export them as CSV. Each overdue statement attracts its own penalty, which is why catching up promptly matters more than getting every category perfect.
If you are more than a couple of quarters behind, the ATO may already have issued a default assessment for a period, which is an estimate it makes when you have not lodged. Lodging the real figures replaces it. If the situation feels out of hand, a registered BAS agent can lodge on your behalf and negotiate with the ATO; the fee is usually modest compared with compounding penalties.
If you have stopped trading
A BAS obligation continues until your GST registration is cancelled, so a business that closed a year ago and never cancelled has four unlodged statements. Lodge nil statements for the periods with no activity, lodge the final one with real figures, and cancel your GST registration with an end date. The obligation stops from that date.
Step 3: make the next one impossible to miss
Most missed statements come from not having the figures ready, not from forgetting the date. Fix the inputs. Upload each month’s statement as it arrives, so the quarter is already categorised on the 1st of the month it is due. Put the four dates in your calendar with a reminder a week before: 28 October, 28 February, 28 April, 28 July. FlowFi emails a reminder seven days and two days out, and the BAS due dates tool shows the next one at a glance. Set aside one eleventh of every payment you receive so the money is there when the statement is.
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Frequently asked questions
Will the ATO fine me for one late BAS?
Possibly, but for an isolated late lodgement with an otherwise clean record the ATO commonly issues a warning or remits the penalty on request. Lodging as soon as you realise is the strongest thing you can do in your favour.
I lodged late but I am due a refund. Is there still a penalty?
The failure-to-lodge penalty is about lodging, not paying, so it can technically apply even to a refund BAS. In practice the ATO rarely pursues it in that situation, and there is no interest because nothing is owed.
Can I lodge a BAS from two years ago?
Yes. Overdue statements stay open in ATO online services until lodged. Prepare the figures from your bank statements for that period and lodge as normal.
General information only, not tax advice. Check your own situation with a registered tax agent or the ATO.
Catch up on a quarter in an afternoon
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