The Australian National University admits to owing staff who were underpaid about $2 million over 11 years.
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The university said a systems error caused underpayments impacting 2290 former and current employees.
The median missed payment per impacted staff member is $600.
In order to be paid, timesheets for casual staff had to be filled out and approved by a supervisor within two weeks.
After a fortnight, the timesheets disappeared.
The university said it had taken steps to rectify the "systems error", which started in 2013 when they moved to online reporting.
A casual staff member raised the issue this year, leading to a greater investigation, the university said.
According to a frequently asked question section on the ANU website the investigation followed a Fair Work Ombudsman inquiry in relation to a casual staff member.
The ANU will pay back money owed with interest and superannuation.
They have already processed 200 payments worth $261,000 from the 2022-23 financial year
The ANU expects the full remediation to be finalised within 10 to 12 weeks.
They said affected staff can expect to be contacted on Thursday afternoon.
The university has also self-reported to the Fair Work Ombudsman and has a website with frequently asked questions.
Another issue was identified when investigating the timesheet issue.
This could potentially affect 120 staff on emergency and on-call duties.
"ANU has engaged KPMG to assist with the investigation and to ensure remediation of any outstanding allowances occurs as quickly as possible," they said.
On its website, the university said the issue would have tax ramifications for impacted staff.
The National Tertiary Education Union said that Australian university staff have now suffered more than $205 million in wage theft.
The wage loss issues were a symptom of an casualised workforce, the union's ACT Division secretary Dr Lachlan Clohesy said.
"Wage theft is a symptom of what is not well in Australia's universities, but the underlying disease is insecure work," he said.
"When workers are employed insecurely, they are less likely to report workplace issues, which is why this can go undetected for so long.
"This is a governance issue which must be addressed by the Australian Universities Accord process."
ANU Vice-Chancellor Genevieve Bell apologised for the error.
"ANU apologises to all staff affected by this error and any hardship, challenges and stress this may have caused," she said.
"ANU is taking immediate and comprehensive action to remedy this situation and to ensure it does not happen again.
"ANU has also notified staff that our investigations have identified as being impacted by this error and is working to remediate all missed payments as soon as possible."
In 2023, the ANU recorded a $27 million shortfall.
Earlier this year, the Australian Catholic University admitted to underpaying over seven years.
It owed $3.6 million to about 100 staff members due to an error in calculating entitlements.
Lanie Tindale
I am City reporter at The Canberra Times. I previously covered health for the masthead, and was a trainee before that. I have written on courts, federal politics, breaking news, features and opinion. lanie.tindale@canberratimes.com.au.
I am City reporter at The Canberra Times. I previously covered health for the masthead, and was a trainee before that. I have written on courts, federal politics, breaking news, features and opinion. lanie.tindale@canberratimes.com.au.
