ATO actively targeting late and unpaid super

The ATO is increasing its scrutiny of employers who pay superannuation late, pay the wrong amount or fail to pay it altogether.

The ATO now compares information reported through Single Touch Payroll (STP) with contribution information reported by superannuation funds. This allows the ATO to identify apparent shortfalls and late payments without waiting for an employee complaint by using STP information to calculate the super due for each employee, and fund data to determine whether the correct amount was received on time.

We are seeing an increasing number of ATO letters advising employers they have compared STP information with data reported by employees’ super funds and identified possible unpaid or late contributions across multiple quarters.

Directors and family members are included

Super obligations are not limited to unrelated employees. They may also apply to directors, family members and other related parties who receive salary, wages or directors’ fees. The ATO is not overlooking late super simply because the person is an owner, director or relative. If super is required, it must be paid correctly and on time.

What is the deadline?

From 1 July 2026, Payday Super applies. Super must generally be received by the employee’s super fund within seven business days after each payday. It is not enough to initiate the payment within seven days. Employers need to allow for payroll, banking and clearing-house processing time. Limited extensions apply in particular circumstances, including certain payments for new employees.

Why even a small delay can be expensive

If the required super is not received in full and on time, the employer can become liable for the Superannuation Guarantee Charge, together with interest, an administrative uplift and potentially further penalties.

The compliance cost can also be significant. Under the former quarterly system, late payments could require a separate SGC statement for every affected quarter. Under Payday Super, the position must be reconstructed for each affected employee and each payday, including:

• what the employee was paid;
• the super that should have been contributed;
• when the contribution was sent;
• when the fund received it;
• whether the fund could allocate it; and
• any rejected or returned contributions.

This means that even a small processing error repeated across several pay runs impacting multiple employees can create substantial payroll reconciliation and compliance costs.

What employers should do

Employers should:

1. Process super at the same time as wages.
2. Check that contributions have been received and accepted by the fund.
3. Investigate rejected or returned contributions immediately.
4. Reconcile payroll records against super fund payment records regularly.
5. Contact their Exant advisor promptly if an ATO letter is received or a late payment is identified.

How Exant Advisory can help

The safest approach is simple: treat super as part of every pay run, not as a bill that can be dealt with later.

If you’d like confidence that your payroll and super processes are compliant, speak with your usual Exant advisor today or alternatively contact our specialist, Nathanael Lee, via the form below or on 07 3218 3900.

A proactive review now could save significant time, penalties and compliance costs later.

Author: Nathanael Lee