You missed a super payment or paid it late¶

It happens. A payday is busy, a payment slips, or money reaches the fund a few days too late. If super for one of your employees was paid late or missed, take a breath. This is fixable, and the most important thing is to sort it out quickly.

There is one thing to understand up front: once super is late, simply paying it into the fund later does not fully close the matter. There is usually a bit more to do.

In one line

If super is late or missed, pay it into the fund as soon as you can — but be aware the ATO can also apply a super guarantee charge, which is more than the original super. Act fast and talk to the ATO.

Why this matters¶

Super is your employee's money for their retirement. When it arrives late, they miss out on time in their fund. The rules treat late super seriously, so knowing what to do protects your employee and helps you avoid a bigger bill later.

What you will learn¶

When super counts as late or missed
Why paying the late super is not the end of the matter
That the ATO can apply a super guarantee charge, and where to get help

Understanding the concept¶

Under the rules that apply from 1 July 2026 (often called Payday Super), you pay super each payday. The ATO explains that super is on time when your employee's fund receives it within 7 business days of the payday, with enough information to put it into the right member's account. The current super guarantee rate is 12%.

The key word is received. Super is only paid when it reaches the fund — not when you send it, and not when it sits with a clearing house. So a payment sent on time can still be late if it reaches the fund after the 7 business days.

If super is late or short, paying the missing amount into the fund is the first step, but not the whole story. The ATO can apply a super guarantee charge (often shortened to SGC). This is a charge worked out and assessed by the ATO. It is more than the super you would have paid, because it also covers interest on the unpaid amount and an extra amount to cover the cost of chasing it up.

The super guarantee charge is different from your ordinary super contributions — it is paid to the ATO, not to the fund, and it is worked out differently. How it is treated for tax has its own rules, so this is a moment to check with the ATO or your accountant rather than guess.

The reassuring part: the ATO has said it will take a supportive approach in the first year, focusing on employers who are not trying to fix things — not on those who pay each payday and fix errors quickly. So acting fast genuinely helps.

For accountants & bookkeepers

Under Payday Super, employers generally no longer lodge a super guarantee statement for a shortfall the way the old quarterly system required. The ATO works out the new super guarantee charge and issues a notice of assessment. The charge is built from the shortfall, notional earnings, an administrative uplift, and any choice loading. The ATO notes that making a voluntary disclosure before it assesses you can reduce the administrative uplift component, and that you may still be liable for the interest and uplift even after the base shortfall is paid. The ATO has said the super guarantee charge for pays from 1 July 2026 can be claimed as a tax deduction — a change from the older charge, which was not deductible. Confirm the current treatment with the ATO for the client's situation.

Example¶

A cafe owner runs a pay run and pays wages on time, but the super for one employee is missed because a fund detail was out of date. The owner spots it a week later. They fix the fund detail and pay the super into the correct fund straight away, so the employee finally receives it. Because it arrived after the 7 business days, the owner also knows the ATO may apply a super guarantee charge, so they contact the ATO to understand what they need to do next rather than assume the late payment alone settles it.

Common mistakes¶

Thinking that paying the super into the fund later fully fixes a late payment — the ATO can still apply a super guarantee charge.
Counting super as "on time" when you send it, rather than when the fund receives it.
Treating the super guarantee charge as if it were the same as your ordinary super — it is paid to the ATO and worked out differently.
Waiting and hoping it will not be noticed, instead of fixing it fast and talking to the ATO.

How this works in myaccountant¶

In the app — myaccountant works out each employee's super in the pay run and shows its status so you can see whether a contribution has been sent and where it is up to. If a contribution needs re-sending, you can pay it again from the payroll super area. The app can help you get the super into the fund, but the super guarantee charge itself is handled with the ATO — myaccountant does not calculate or pay it for you.

Key points¶

Super is on time only when the fund receives it within 7 business days of payday.
Paying late super into the fund is the first step, not the whole fix.
The ATO can apply a super guarantee charge, which is more than the original super.
The super guarantee charge is separate from ordinary super — it is paid to the ATO and has its own tax treatment.
Acting fast helps — the ATO focuses on employers who do not fix errors.
For anything about the super guarantee charge, contact the ATO or your accountant.

Learn next¶

General information only — not tax, super or financial advice.

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