What does payday super change for late super?

Old rules versus new rules at a glance

The Small Business Superannuation Clearing House closed to new users on 1 October 2025 and shut completely on 1 July 2026, so employers who relied on it need another clearing house or payroll software that pays super each run.

What gets easier

• A quick fix costs little. Notional earnings only run for the days you were late, and paying the contribution stops them. A voluntary disclosure within 30 days cuts the uplift by up to 40 percentage points, and a clean 2 year history cuts a further 20, so a prompt correction can carry no uplift at all.
• Most of it is deductible. The shortfall, notional earnings and uplift are all deductible. Under the old rules, nothing in the SGC was deductible.
• No more forgotten statements. The ATO assesses the charge from Single Touch Payroll and fund reporting. Employers can no longer lose penalty remission simply by missing a lodgement date.
• First year leniency. The ATO has said that in 2026-27 it will not focus compliance action on employers who tried to pay each pay day and fixed problems as soon as reasonably practicable.

What gets harder

• The deadline is measured in days, not months. A weekly payroll now has 52 deadlines a year, and each one is met only when the fund receives the money.
• The ATO knows quickly. Payroll data and fund data are matched continuously, so an unpaid pay run is visible within weeks rather than at the end of a quarter.
• Ignoring an assessment is expensive. If the charge is not paid within 28 days the ATO sends a notice to pay. Another 28 days of silence adds a late payment penalty of 25% of the charge, or 50% if you had the same penalty in the previous 24 months. That penalty cannot be remitted, and GIC accrues on the unpaid charge.
• Director liability still bites, and the timing rules changed. The director penalty attaches to the assessed charge. Under the amended rules the penalty is understood to lock down unless the shortfall was disclosed to the ATO within a short window after the pay day, and before the ATO raised its own assessment. Read am I personally liable for unpaid super before assuming a restructure will clear it.

The changeover trap for the June 2026 quarter

The April to June 2026 quarter was due on 28 July 2026 under the old rules. If it was late, the old regime applies in full: lodge an SGC statement by 28 August 2026, pay a non deductible charge, and note that the late payment offset is not available for that quarter. Contributions received on or after 29 July 2026 are applied to payday super pay days, not to the old quarter. If you are catching up on both old and new periods, work out the order of payments with your accountant, and if the total is more than you can pay at once, ask the ATO for an ATO payment plan early rather than waiting for a notice.

What to do next

1. Check that your payroll or clearing house sends super with every pay run and confirm the fund receipt date for the first few cycles.
2. If a pay day since 1 July 2026 was missed, pay the shortfall now and lodge a voluntary disclosure within 30 days.
3. Deal with any late quarter up to June 2026 separately: lodge the SGC statement by its due date and pay or arrange a plan.
4. If a company owes super under either regime, get advice on the director penalty position before deciding on any restructure.

More questions: 8 Super guarantee charge questions questions answered · Full guide: Super guarantee charge (SGC)