Key Highlights

  • The new super guarantee charge applies to super guarantee for qualifying earnings days from 1 July 2026, according to the ATO's explainer on the charge.
  • The first is the individual final super guarantee shortfall, which is the super guarantee still unpaid when the ATO makes its assessment.
  • Under the old rules, employers who missed a quarterly payment were expected to work out the charge themselves and lodge a statement.
  • The ATO now assesses the super guarantee charge and issues a notice of assessment, according to the Tax Office.

Employers who fall behind on super now face a rebuilt super guarantee charge, with interest set at the ATO's general interest charge rate, an administrative uplift the ATO says starts at 60%, and a late payment penalty that cannot be remitted. The first quarter of the new regime ended on 30 September 2026, and the interest rate behind the charge rose to 11.51% on 1 October, making the cost of falling behind a live question now.

The Four Parts of the New Charge

The new super guarantee charge applies to super guarantee for qualifying earnings days from 1 July 2026, according to the ATO's explainer on the charge. It is calculated for each qualifying earnings day and has four components.

The first is the individual final super guarantee shortfall, which is the super guarantee still unpaid when the ATO makes its assessment.

The second is notional earnings. These apply the general interest charge rate to the base shortfall, compounding daily. The ATO lists the general interest charge at 11.51% a year for October to December 2026, up from 11.43% in the previous quarter.

The third is the administrative uplift. The ATO says it "starts at 60%" of the shortfall plus notional earnings. Regulations can reduce the uplift, including to nil, and the ATO's explainer said none had been made when it was published in November 2025. Elsewhere, the ATO has said the uplift varies with an employer's compliance history and whether it made a voluntary disclosure.

The ATO Now Assesses the Charge

Under the old rules, employers who missed a quarterly payment were expected to work out the charge themselves and lodge a statement. That has changed.

The ATO now assesses the super guarantee charge and issues a notice of assessment, according to the Tax Office. If the charge is unpaid within 28 days, the ATO must issue a Notice to Pay.

The shift puts the ATO in the driver's seat. It draws on Single Touch Payroll and SuperStream data to identify shortfalls, rather than relying on employers to come forward.

Clearing houses do not shift the risk. Accountants Daily has reported that under Payday Super, employers are liable for late payments caused by clearing house delays.

The Penalty That Cannot Be Remitted

If the amount in a Notice to Pay is still outstanding after 28 days, a late payment penalty of 25% of the outstanding charge applies. That rises to 50% if the same penalty has applied to the employer in the previous 24 months.

The ATO says this penalty "cannot be remitted". That is a sharp break from the old regime, under which penalties of up to 200% could apply but could also be remitted by the Commissioner.

The tax treatment also differs. Under the new rules, the super guarantee charge paid is tax-deductible, but the general interest charge and the late payment penalty are not.

That follows a broader change. General interest charge incurred from 1 July 2025 is no longer deductible for any tax debt. Tax Commissioner Rob Heferen put the ATO's view plainly at a CPA Australia forum in August: "The tax office should not be thought of as a source of finance."

A Hypothetical Worked Example

Applying a 60% administrative uplift to that base adds about $6,173. The total charge assessed would be about $16,460, or roughly 1.65 times the original shortfall.