- Lodge overdue BAS and company returns now, oldest first, even if you can't pay.
- Nil or refund statements generally attract no late-lodgement penalty notice.
- Report GST and PAYG withholding within 3 months to protect directors.
- Tax debts of AUD 200,000 or less can usually go on an online payment plan.
If you have overdue company tax returns or BAS, lodge every outstanding statement as soon as you can, oldest first, even if you can’t pay yet. A registered tax agent, such as the team behind Sleek’s catch-up service, can see your full lodgement list, deal with the ATO for you and set up a payment plan before penalties, interest and director liability grow. The good news: late statements with a nil or refund result generally don’t attract a late-lodgement penalty notice, and tax debts of AUD 200,000 or less can usually go on a payment plan online.
Behind on tax returns or BAS? What should you do first?
Stop the gap from growing, then work backwards through the backlog. Being behind is more common than most owners think, and it is fixable once you know exactly what is outstanding.
Three things to do this week:
- Find out exactly what’s overdue. Log in to Online services for business, or nominate a tax agent who can see your company’s full lodgement list and account balance.
- Lodge the next BAS on time, even if you can’t pay it. A fresh late BAS lodgement on top of an old backlog only adds penalties, and lodging and paying are separate steps.
- Gather your records. Pull bank statements, Xero or other software files, payroll reports and past BAS. Gaps aren’t a blocker, because missing records can usually be rebuilt.
How do you catch up on overdue company lodgements?
Whether you need to catch up on BAS, company returns or both, the process is the same five steps: list it, reconcile it, lodge it, deal with the debt, then stop it happening again. Work through them in order, because each step feeds the next.
- List every overdue lodgement. Include each BAS, every company tax return, PAYG withholding and Single Touch Payroll (STP) reports, and any super guarantee payments.
- Reconcile your bank and Xero. Match every transaction to the bank so the figures you lodge are right. If the books are months behind, catch-up bookkeeping does this in bulk.
- Lodge oldest first. Earlier periods feed the figures in later ones, so lodging in date order keeps each return accurate.
- Pay, or set up a payment plan. Pay what you can and put the rest on an ATO payment plan, which most businesses can arrange online.
- Set a schedule so it doesn’t recur. Put your tax due dates in a shared calendar and agree who lodges what.
If you want to see how BAS is lodged field by field, Sleek’s step-by-step guide covers it. The table below shows what each overdue item risks and who can fix it.
| What’s overdue | Risk if it stays overdue | First action | Who can do it |
|---|---|---|---|
| BAS (GST and PAYG withholding) | Late-lodgement penalties, GIC on unpaid tax, and director penalties if not reported within 3 months | Lodge the current BAS on time, then the backlog oldest first | You, a registered BAS agent or a registered tax agent |
| Company income tax return | Late-lodgement penalties, a possible default assessment and refunds held back | Reconcile the year’s books and lodge the oldest year first | A registered tax agent |
| STP and payroll reports | Late-lodgement penalties and wrong employee income statements | Correct and lodge missing pay events through your payroll software | You, or your BAS or tax agent |
| Super guarantee | Super guarantee charge, which directors can become personally liable for | Pay outstanding super and check the Payday Super deadlines | You, with your payroll provider or agent |
| ASIC annual review | ASIC late fees, which are separate from the ATO | Pay the review fee and confirm the company’s details | You or an ASIC registered agent |
Can a tax agent help with the ATO?
Yes. Once you nominate a registered tax agent, they can see your company’s full lodgement and account position and deal with the ATO on your behalf.
A registered tax agent can:
- see every outstanding lodgement and the balance of each ATO account
- prepare and lodge overdue BAS and company returns for you
- request an ATO lodgement deferral where there’s a genuine reason, such as a newly engaged agent needing more time on a backlog
- set up a payment plan for debts you can’t pay straight away
- help you ask for remission of late-lodgement penalties once the outstanding documents are lodged
An ATO lodgement deferral moves a due date; it doesn’t cancel the lodgement. Deferrals and remission are never automatic, because the ATO decides each request on its merits, so no agent can promise an outcome.
The difference an agent makes is speed and accuracy: one person who knows the ATO’s process works through the backlog in the right order.
What does waiting cost?
Each overdue document can attract a failure to lodge on time (FTL) penalty of one penalty unit for every 28 days (or part of 28 days) it is late, capped at five units. On top of that, the general interest charge (GIC) runs daily on any tax you haven’t paid.
The ATO says it generally doesn’t penalise an isolated late lodgement, and it warns you by phone or in writing before it applies an FTL penalty. A backlog of several periods is a different story, which is why acting before that warning arrives matters.
The penalty unit is AUD 364 for failures on or after 1 July 2026, AUD 330 from 7 November 2024 to 30 June 2026, and AUD 313 from 1 July 2023 to 6 November 2024. Medium withholders pay double the base amount and large withholders pay five times (ATO penalty units table, checked 9 November 2026).
Here’s what that looks like at the current AUD 364 unit, for a company whose statements aren’t nil or refunds:
| Late lodgement | Small entity | Medium withholder (x2) | Large withholder (x5) |
|---|---|---|---|
| 1 BAS, four months late (5 units) | AUD 1,820 | AUD 3,640 | AUD 9,100 |
| 4 BAS, each 6+ months late (5 units each) | AUD 7,280 | AUD 14,560 | AUD 36,400 |
| Company tax return, 1 year late (5 units) | AUD 1,820 | AUD 3,640 | AUD 9,100 |
Every late BAS lodgement is penalised separately, so a backlog adds up quickly. A backlog spanning several years mixes unit values, so ask your agent to check each document against the date it fell due.
Interest is the cost that keeps climbing. At 11.51% a year (the GIC rate for October to December 2026, compounding daily), AUD 20,000 of unpaid GST costs roughly AUD 1,180 in interest over six months.
The relief: a late company tax return or BAS with a nil or refund result generally gets no FTL penalty notice. The exceptions are large withholders, penalties applied before you lodge, and third-party reports such as the taxable payments annual report. For every other penalty type, see Sleek’s full list of ATO penalties.
When does overdue BAS become a director’s problem?
When the company leaves PAYG withholding, GST or super guarantee charge unpaid, directors can become personally liable for it. The ATO can recover those amounts from you 21 days after it issues a director penalty notice (DPN).
Timing matters most. If the company reports PAYG withholding or GST within three months of the due date, a DPN can still be remitted by paying in full, appointing an administrator or small business restructuring practitioner, or starting to wind the company up. Report later than three months, or never (ATO estimates count as never reported), and paying the debt in full is the only way out.
That’s why lodging matters even when the bank account is empty. Most director penalty problems start with a BAS nobody lodged, not with a debt nobody could pay. Once a DPN issues, an overdue BAS that company directors have left unreported for more than three months can only be cleared by paying it in full.
Resigning doesn’t make the problem go away. You stay liable for amounts that relate to your time as a director, even after the company is deregistered.
New directors have 30 days from appointment to deal with debts that arose before they joined, or they can inherit the liability. Super adds a second deadline: since 1 July 2026, under Payday Super, contributions must reach each employee’s fund within 7 business days of payday (20 business days for a new employee’s first contribution).
If you’ve received a DPN, don’t wait out the 21 days. Get professional advice straight away, including insolvency advice if the company can’t pay its debts.
How much does it cost to catch up?
There are two parts: a one-off catch-up fee and the ongoing plan that keeps you current. Sleek reviews everything outstanding, then scopes and quotes the catch-up work upfront as a separate one-off, so you know the cost before any work starts.
Most catch-ups cost between AUD 400 and AUD 3,200. Of the 158 Australian companies that paid Sleek for catch-up work in 2026, 8 in 10 paid within that range and the median was AUD 1,000. A single nil return sits at the low end, while several years of books, BAS and returns sit at the top.
Once you’re up to date, an ongoing company accounting plan keeps future lodgements on track, from AUD 275 a month (sleek.com/au, checked 9 November 2026). If you’d rather compare options first, see what an accountant for small businesses typically includes.
If the tax itself is the problem, an ATO payment plan set up early spreads the debt, though GIC keeps accruing. Compare the one-off catch-up fee with the cost-of-waiting table above: the fee is paid once, while penalties and interest keep growing.
What if your accountant left you behind?
Many companies fall behind because their accountant went quiet, not because the owner ignored the ATO. Of the 158 Australian companies that paid Sleek for catch-up work in 2026, 133 (84%) had moved over from another provider. Moving to a new agent mid-backlog is common and doesn’t mean starting from scratch.
The handover usually runs like this:
- You nominate the new agent through Online services for business, or the agent adds your company to their client list.
- The new agent requests your records and prior returns from your old accountant.
- The new agent reviews what’s outstanding and starts the catch-up.
If you gave your agent everything they needed on time and they still didn’t lodge, the ATO’s safe harbour rule may mean you aren’t liable for the FTL penalty. That protection doesn’t extend to director penalties, though: courts have held that relying on an accountant is not a defence to a DPN.
Sleek’s guide to switching accountants explains what to ask your old accountant for and how to avoid gaps in the handover.
What happens if you leave it?
Penalties and interest keep growing, and the ATO has firmer tools it can use. It may issue a default assessment or an estimate of what you owe, hold back refunds, and move to recover the debt.
Every late company tax return also makes finance harder, because lenders usually ask for up-to-date returns and BAS. Directors carry the DPN risk covered above, and if the business has wound down, read what to do if the company has stopped trading.
How does Sleek’s catch-up service work?
Sleek’s registered tax agents (TPB agent number 26131380) follow four steps: review, quote, lodge, then keep you current. It’s built for companies that need to catch up on BAS and overdue company tax returns without chasing the ATO themselves.
- Review. Once nominated as your agent, Sleek reviews your full lodgement list and flags anything time-sensitive, such as a director’s BAS penalty notice deadline.
- Quote. You get a quote for the one-off catch-up work before anything starts.
- Lodge. The overdue lodgements in your quote are prepared and lodged, oldest first.
- Stay current. An ongoing plan keeps future lodgements on time.
Of the companies that paid for catch-up work in 2026, about half needed only an overdue company tax return lodged, around a third needed BAS or bookkeeping, and nearly 1 in 5 had more than one financial year to clear. Eight in 10 also have an ongoing accounting plan with Sleek.
Start with Sleek’s catch-up service and a short review of where your company stands.
Last reviewed 9 November 2026 by Colin Lua, CPA Australia member and Registered Tax Agent. ATO figures and Sleek prices were checked on ato.gov.au and sleek.com/au that day; Sleek client figures cover AU payments from 1 January to 5 November 2026.
Ready to get your company back on track?
450,000
businesses worldwide.
from 4,100+ reviews.
FAQs on overdue company tax returns
Is the tax return included in the catch-up price, or is it extra?
The catch-up work is scoped and quoted upfront as a separate one-off, so you can see what it covers before you agree to it. Depending on what’s overdue, it can cover bookkeeping, BAS, company tax returns, and payroll or unpaid super. Lodgements after you’re up to date fall under your ongoing accounting plan, not the catch-up quote.
Should I lodge the oldest year first?
Usually, yes. Each year’s return relies on figures from the year before, such as tax losses carried forward and PAYG instalment amounts, so lodging in date order keeps every return accurate and avoids amendments later. Your agent may lodge the current BAS first to stop the gap growing, then work back through the backlog.
Can I get a payment plan for the tax I owe?
Yes, for most business debts. If your company owes AUD 200,000 or less, you may be able to set one up in Online services for business or through the ATO’s self-help phone line, and your registered tax or BAS agent can do it for you. Debts over that amount, or plans longer than two years, need a call to the ATO. GIC keeps accruing until the debt is paid.
Will the ATO cancel penalties if I catch up?
Not automatically. The ATO can remit all or part of a failure to lodge penalty based on your circumstances, but it expects you to lodge your outstanding documents before you ask. Lodging quickly is usually the most effective way to limit what you owe.
What if I don't have all my records?
Missing records aren’t a blocker. Bank statements, ATO pre-fill data, supplier invoices, payroll reports and past BAS can usually rebuild a year’s figures, and your agent will flag any gaps that need extra evidence.
Can you take over from my current accountant mid-catch-up?
Yes. You nominate Sleek as your tax agent, and your records and prior returns are requested from your current accountant. Anything already lodged stays lodged, so the catch-up only needs to cover the periods still outstanding.
