Highlights

  • The final June-quarter super guarantee payment 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.
  • The late payment offset is not available for this final quarterly obligation.
  • As of 9 September 2026, the 28 August SGC deadline has already passed, so unresolved cases are now overdue and should be addressed promptly.

Tax agents whose employer clients missed the final quarterly super guarantee deadline have been given clear guidance by the Australian Taxation Office on what to do next.

The June 2026 quarter super contribution was due to reach employees' funds by 28 July 2026. With Payday Super now in force, the treatment of a missed final quarterly payment differs from the approach employers may have used in earlier periods.

Because it is now 9 September 2026, both the original quarterly payment deadline and the subsequent SGC lodgment and payment deadline have already passed. Any employer client who has not yet dealt with the shortfall should therefore treat the matter as overdue and act promptly.

Lodge an SGC statement

If an employer client did not get the required June-quarter contributions to employees' funds by 28 July 2026, the client entered the super guarantee charge process.

The SGC statement and payment were due to the ATO by 28 August 2026.

The important distinction is that the SGC is paid to the ATO rather than directly to the employee's super fund.

For clients who still have an outstanding obligation now, agents should focus on completing the required SGC process rather than assuming that a late direct contribution to the fund will resolve the original quarterly shortfall.

No late payment offset

The ATO has confirmed that the late payment offset is not available for this final quarterly payment.

Under earlier arrangements, a late contribution could sometimes be used to reduce an SGC Liability where the relevant conditions were satisfied.

That option does not apply to the final June 2026 quarterly obligation.

This means agents should not rely on the treatment available in earlier quarters when advising affected employer clients.

Beware the Payday Super transition

The transition to Payday Super creates an additional complication.

Contributions received by a super fund on or after 29 July 2026 are dealt with under the Payday Super framework rather than automatically being treated as catch-up payments for the June-quarter shortfall.

That means an employer who paid the fund late may still have an outstanding SGC obligation for the June quarter.

Agents should therefore confirm:

  • when the original contribution was submitted;
  • when the fund actually received it;
  • whether any payment was made after 28 July; and
  • how that payment was allocated.

The date of receipt by the fund is critical.

What the SGC involves

The super guarantee charge can be more expensive than making the original super contribution on time.

It includes:

  • the super guarantee shortfall;
  • a nominal interest component; and
  • an administration fee.

The SGC calculation can also be based on total salary and wages rather than the ordinary time Earnings measure used for normal super guarantee contributions.

The charge is also not tax deductible.

For clients, that means missing the deadline can create both a compliance issue and a higher financial cost.

Who may be affected and what to do

Employer clients who did not get the full June-quarter contribution to employees' funds by 28 July 2026 are directly affected.

Tax agents should identify any clients with unresolved June-quarter shortfalls and help them determine whether an SGC statement remains outstanding.

Because the 28 August deadline has already passed, affected clients should not wait for further ATO contact before taking action.

Agents can add value by reviewing Payroll records, clearing-house reports and fund receipt dates to establish exactly what happened.

The transition has closed old options

The ATO's guidance reflects the shift from quarterly super to Payday Super.

Previously, employers sometimes had more flexibility to make late contributions directly to a fund and use the late payment offset against an SGC liability.

For this final quarterly payment, that pathway is not available.

At the same time, contributions received from 29 July fall into the new Payday Super allocation framework.

That creates a genuine risk that an employer who tried to "catch up" by paying the fund late may still owe the SGC for the June quarter.

The employer could therefore end up with both a fund payment and an SGC liability if the transition rules are misunderstood.

Guiding clients through the SGC process

Agents should help affected clients establish the size of the shortfall, complete the SGC statement and address any amount owing to the ATO.

The key documents to review include:

  • payroll records for the June quarter;
  • employee salary and wage information;
  • super payment records;
  • clearing-house reports;
  • fund receipt dates; and
  • any contributions made after 28 July.

Interest continues to be relevant while an SGC liability remains unresolved, so delay can increase the cost.

Clear advice now can also help clients improve their systems under Payday Super, where payment timing is much tighter than under the old quarterly system.

What agents should prioritise now

Given that the relevant deadlines have already passed, the priority is no longer preparation but remediation.

Agents should identify affected clients, confirm whether the June-quarter super was actually received on time, and determine whether an overdue SGC statement or payment remains outstanding.

They should also check whether any late fund payment was incorrectly assumed to have fixed the June-quarter shortfall.

The broader lesson is that under Payday Super, receipt timing, allocation and rejected payments need to be monitored far more closely.