At least 60 federal MPs' junior staff have been underpaid over the past four years with the Finance Department admitting the error.
The department identified periods since 2017 where the rate paid to some electorate officers was less than the award.
The employees affected earn between $51,000 and $68,000 a year.
The underpayments have sparked a KPMG audit to look into all staff pay over the past four years, including former employees.
"We expect this audit will be completed and back pay will be made to all affected staff by the end of the current financial year," the department told staff in an email.
"We will be contacting all affected staff directly."
Finance self-reported the issue to the Fair Work Ombudsman and notified the Community and Public Sector Union and Australian Services Union.
