Two years of overdue BAS: how to catch up, and what it costs

Let 2Fin do the boring bits

Catching up is mostly sorting, and sorting is the part 2Fin takes off you. Bring in two years of bank statements at once — CSV, Excel or PDF, several files in one go — and Fin reads every line; in testing, 1,891 transactions came in in about a second on a desktop computer. Each transaction is categorised with its GST or VAT worked out, every overdue quarter is listed with its due date, and Fill all periods saves a draft of each one with a single press.

What is left for you is the decisions, not the data entry. Purchases are grouped by payee — in the timed run, 1,574 purchase rows became 30 payees — so you answer each payee once and the answer covers every quarter. Fin’s confident guesses (80% sure or more) can be accepted in one tap and undone one by one, and a payee can become a rule so the next import sorts itself. Every figure opens to the transactions inside it, and the finished statements export for you or your agent to check and lodge.

What happens if you don’t lodge your BAS

The ATO writes first. If statements stay outstanding it can issue a final notice, then a default assessment of the GST it thinks you owe, with a penalty of up to 75% of that amount, and ultimately prosecution. Lodging, even late, replaces all of that with your own figures and a capped late-lodgment penalty.

The ATO also says it generally does not apply the failure-to-lodge penalty to an isolated late lodgment, warns you before it does, and generally does not penalise a late nil or refund BAS. A catch-up lodged before the ATO contacts you is the cheapest version of this problem.

The failure-to-lodge penalty, worked through

The penalty is one penalty unit for every 28 days (or part of 28 days) a BAS is late, up to five penalty units for a small business. A penalty unit is $364 for lateness from 1 July 2026, so a single quarterly BAS that is 5 months late reaches the cap: 5 × $364 = $1,820. Medium businesses ($1 million to $20 million GST turnover) pay double; large businesses five times.

Across eight overdue quarters that could in theory reach eight caps, which is why the remission request matters. The ATO considers remission once your outstanding statements are lodged, and lists severe illness, natural disaster and family violence among the reasons it is likely to accept. This is general information. Check what applies to you with a registered tax or BAS agent, or with the tax office.

The order to lodge in

Lodge the earliest quarter first. The ATO asks that the first activity statement of a financial year be lodged before the later ones, and keeping them in order keeps your GST registration date, credits and any PAYG instalments in sequence. Every overdue BAS can be lodged through Online services for business; an overdue nil BAS can also be lodged by phone, up to three at a time.

A registered BAS agent lodging electronically gets later due dates for current quarters under the ATO’s lodgment program, which is worth knowing if you hand the prepared figures to an agent for the final check.

Rebuilding eight quarters from a bank file

Most catch-ups start with no bookkeeping at all, just bank accounts. Download two years of statements as CSV, Excel or PDF. The sales side of each quarter is the business money in; under Simpler BAS, the default for GST turnover under $10 million, that becomes G1 (total sales) and 1A (GST on sales). The purchases side becomes 1B (GST credits), and that is where your judgement is needed.

In 2Fin the steps are: import the file; enter the date the business registered for GST, and Fin lists every quarter not yet lodged with its due date and status; press Fill all periods to save a draft for each; then answer the purchases review. The review groups every purchase by payee — in the timed run, 1,574 purchase rows became 30 payees — and one answer (all business, part business with a percentage, private, or a capital purchase) applies to every quarter at once. Nothing is applied until you tap, and every answer can be undone.

Purchases: claim what you can prove

You need a tax invoice to claim the GST credit on any purchase over $82.50 including GST, and a supplier has to give you one within 28 days of asking. For purchases at or under $82.50 a receipt or docket is enough. Where something was partly private — a phone, the internet, a car — claim only the business share. In 2Fin, a purchase with no tax invoice yet can be answered No tax invoice: it stays a business cost and its GST credit is held back until you find the invoice.

Claim missed credits while they are in date: they expire 4 years after the original BAS was due, and lodging an amendment does not stretch that. Where you are unsure whether a purchase was for the business, leave it out until you are sure; a missed credit can go in a later BAS within the time limit. This is general information. Check what applies to you with a registered tax or BAS agent, or with the tax office.

If you can’t pay what the BAS shows

Lodge anyway, then set up a payment plan. Smaller debts can be set up through Online services for business or the ATO’s self-help phone line; larger debts, or a plan longer than two years, need a call. The general interest charge keeps accruing on a plan, compounding daily at 11.51% a year for October–December 2026, and since 1 July 2025 it is not tax-deductible, so a shorter plan costs less.

If any quarter was under-reported in a BAS you already lodged, correcting it before the ATO asks is treated as a voluntary disclosure, which the ATO says is likely to reduce penalties and interest.

Never registered, but over $75,000?

You had 21 days to register after your GST turnover reached $75,000. Registering late can mean paying GST on sales from the date you should have registered, even where you didn’t include GST in the price, plus penalties and interest. Backdating is generally limited to 4 years and is arranged by phoning the ATO’s business line. Raise this before lodging any catch-up BAS, because it decides which quarters you owe. This is general information. Check what applies to you with a registered tax or BAS agent, or with the tax office.

How the time was measured

The times on this page come from one recorded run on 10 November 2026, not from a survey of users. The test case was a GST-registered sole trader with a salaried job on the side: two years of bank history, 1,891 transactions, and eight quarterly BAS not yet lodged. The file was imported into the 2Fin app and each quarter prepared from it, on a desktop computer.

The computer’s share — reading the file, categorising every row and filling all eight quarters — took under 3 minutes. The person’s share is modelled rather than stopwatched: 2.5 seconds for each tap and about 6 seconds to decide each payee. On that model the first quarter’s sales figures (G1 and 1A) take about 3 minutes and 18 actions, and all eight quarters, purchases included, take 7.5 to 11.5 minutes. A first-timer reading every screen will be slower; someone who knows their payees, faster.

Purchases are where the checking is. Fin grouped the 1,574 purchase rows into 30 payees, and one answer per payee (all business, part business, private, or a capital purchase) applied to every quarter at once. In that run the eight quarters’ GST credits (1B) came to $1,707.77 against the test’s answer key of $1,500.00, about 14% high; the gap matched the GST on two phone and internet payees answered as 50% business use, which the answer key left out. That is why the figures are prepared for your review, and why every BAS figure in 2Fin opens to show the transactions inside it.