One of Australia’s biggest universities has been caught up in an $11 million wage underpayment scandal affecting more than 16,000 current and former staff.

The University of Queensland (UQ) has signed an enforceable undertaking with the Fair Work Ombudsman (FWO) after underpayments spanning almost a decade were uncovered across its Brisbane and Gatton campuses.

The payroll bungle occurred between 2017 and 2026 and affected 16,382 academic and professional staff, the workplace watchdog said on Tuesday.

Know the news with the 7NEWS app: Download today

One employee was owed $41,643, including interest and superannuation. The smallest underpayment less than a dollar, while the average amount owed was $564.

The total includes about $9.2 million in unpaid wages, $1.02 million in superannuation, $427,000 in interest and about $315,000 in interest on superannuation.

The affected employees worked at UQ’s St Lucia, Herston and Dutton Park campuses in Brisbane, as well as its Gatton campus in the Lockyer Valley, east of Toowoomba.

The University of Queensland has already repaid more than $9.6 million to thousands of affected current and former employees. Credit: University of Queensland

Just over a quarter of those affected came from the university’s Health, Medicine and Behavioural Science faculty.

UQ has already paid more than $9.6 million — including superannuation and interest — to 13,514 current and former employees, with the undertaking requiring payments to the remaining staff.

The university said it had proactively alerted the Fair Work Ombudsman in 2021 after identifying areas of “unintentional non-compliance” with its enterprise agreements dating back to 2017.

“I would like to sincerely apologise again to current and former staff,” a UQ spokesperson told 7NEWS.com.au.

A review, now complete, identified underpayments relating to minimum engagement periods, overtime arrangements and rates for casual academic staff with a PhD.

“Although unintentional, this does not reflect our commitment to our people and the University will ensure that affected staff will receive all back pay, including superannuation and interest,” the spokesperson said.

Most repayments had already been made, UQ said, with affected staff receiving backpay between 2019 and 2024.

The university said it would contact staff still owed money in the coming weeks to remediate outstanding amounts.

The university first alerted the regulator in October 2021 that it would launch an external review into whether it was correctly applying its enterprise agreements.

Fair Work Ombudsman Anna Booth said the case highlighted the importance of getting payroll systems right from the outset.

“The Enforceable Undertaking with the University of Queensland highlights the importance of universities improving their governance over payroll and administrative systems, to ensure employees are paid correctly from the start of, and throughout, the term of a uni’s own enterprise agreement,” Booth said.

As part of the undertaking, UQ will also make a $175,000 contrition payment to the Commonwealth’s Consolidated Revenue Fund.

Fair Work Ombudsman Anna Booth has signed an Enforceable Undertaking with the University of Queensland over about $11 million in staff underpayments. Credit: FWO/7NEWS

The university said it was implementing improved systems and processes, compulsory training, enhanced assurance checks and an independent audit to prevent similar failures happening again.

“We acknowledge that the University of Queensland reported these underpayments to us and has been dedicated in taking action to rectify them and prevent future non-compliance impacting their staff,” Booth said.

The latest case follows a string of university underpayment matters around the country, including in Queensland, where CQUniversity recently rectified more than $1.3 million in underpayments to more than 1000 employees.

In earlier cases, the Fair Work Ombudsman has also secured court penalties against the University of Melbourne and UNSW over staff payment and workplace entitlement breaches.