Highlights

  • The final quarterly super guarantee payment for Earnings from April to June 2026 had to reach employees' funds by 28 July 2026.
  • Employers who missed that deadline were required to lodge a super guarantee charge statement and pay the SGC to the ATO by 28 August 2026.
  • The late payment offset is not available for this final quarterly obligation.
  • Contributions received by super funds from 29 July 2026 are allocated under the Payday Super framework rather than retrospectively fixing the June-quarter shortfall.

The transition to Payday Super changed how employers need to deal with a missed final quarterly super payment.

The last quarterly super guarantee payment, covering qualifying earnings paid between April and June 2026, needed to be received by employees' super funds by 28 July 2026. Employers who missed that deadline moved into the super guarantee charge process rather than simply making a late quarterly contribution.

Because both the 28 July payment deadline and the 28 August SGC deadline have now passed as of 9 September 2026, affected employers should treat any outstanding obligation as overdue and act promptly.

Do not simply pay the fund

If an employee's super fund did not receive the full June-quarter contribution by 28 July, the ATO's transition guidance says the employer must deal with the shortfall through the super guarantee charge regime.

For the final quarterly obligation, employers who missed the deadline were required to lodge an SGC statement and pay the SGC to the ATO by 28 August 2026.

That deadline has now passed, so an employer that has still not lodged or paid should not assume that making a normal contribution directly to the employee's fund will resolve the earlier quarterly shortfall.

Why paying the fund can backfire

The transition rules determine how super payments made around the changeover are allocated.

Payments received by a fund between 1 July and 28 July 2026 were first applied to outstanding June-quarter amounts. Any balance could then be applied under Payday Super.

However, contributions received on or after 29 July 2026 are allocated to Payday Super amounts, even if the employer intended the payment to cover the earlier June-quarter liability.

That means a late payment made directly to the fund after the cut-off does not retrospectively eliminate the employer's SGC obligation for the final quarterly period.

An employer could therefore still owe the SGC despite having subsequently transferred money to the employee's fund.

No late payment offset this time

The ATO has specifically confirmed that the late payment offset is not available for the final June 2026 quarterly super obligation.

Under the previous framework, qualifying late contributions could in certain circumstances be offset against an employer's super guarantee charge.

For the transition to Payday Super, however, that relief does not apply to the final quarterly payment.

This is an important distinction because employers should not assume the treatment available for earlier quarters continues unchanged.

Who may be affected

The issue affects employers whose full April–June 2026 super guarantee contributions were not received by their employees' funds by 28 July 2026.

It can also affect employers who attempted to rectify the position after 28 July by making contributions directly to employees' funds.

Because payments received from 29 July are dealt with under the Payday Super allocation rules, a late contribution may not have the effect the employer intended.

Employers should therefore check when the fund actually received the contribution rather than relying only on the date the payment was submitted.

What to consider next

For employers still dealing with a June-quarter shortfall, the immediate priority is to determine whether an SGC statement remains outstanding and calculate the amount payable.

The original SGC lodgment and payment deadline was 28 August 2026. Since that date has now passed, further delay can increase the employer's compliance exposure.

Employers should also review contributions made from 29 July onwards to understand how those amounts were allocated under Payday Super.

Clear payroll, clearing-house and fund records will be important in establishing what was paid, when it was received and which obligation the payment satisfied.

Why the process has changed

The special treatment reflects the transition from quarterly super guarantee payments to Payday Super.

Under the previous framework, employers generally had quarterly deadlines and could sometimes use a qualifying late payment against an SGC liability.

From 1 July 2026, super for new qualifying earnings moved to the Payday Super system, with contributions generally required to reach the employee's fund within seven Business days of payday.

The transition therefore created an overlap during July: employers could have final June-quarter liabilities alongside new Payday Super obligations.

To manage that overlap, contributions received up to 28 July were first applied to outstanding quarterly amounts, while payments received from 29 July are treated under the new framework.

The SGC can cost more than paying on time

Missing the super guarantee deadline can be more expensive than making the original contribution on time.

The super guarantee charge includes the relevant shortfall together with interest and an administration component.

The calculation also differs from ordinary on-time SG because the shortfall can be based on a broader earnings measure than ordinary time earnings.

Employers should therefore not treat the SGC simply as a delayed version of the contribution they originally intended to make.

What employers should do now

As of 9 September 2026, both transition deadlines have passed.

An employer that missed the 28 July contribution deadline and has not completed the SGC process should establish the outstanding Liability promptly, lodge any required statement and address the amount owing.

Employers that made a direct fund payment after 28 July should also check how that contribution was allocated rather than assuming it corrected the quarterly shortfall.

The broader lesson from the transition is that the date on which the super fund receives a contribution matters. Under Payday Super, payment timing and rejected contributions require closer monitoring because the system now operates on a much shorter cycle.