Non-profit provider Goodwin Aged Care Services self-reported the underpayment of more than 300 mostly migrant staff between 2018 and 2025.
313 staff affected were party to unsatisfactory terms which were "over-reliant" on non-monetary benefits, while 22 staff were incorrectly paid afternoon shift penalties.
Goodwin said it has taken action to prevent similar future issues, and has paid back affected staff wherever possible.
An aged care provider in the ACT and NSW has been ordered to back pay more than $1.3 million to 335 employees, as part of an enforceable undertaking with the Fair Work Ombudsman.
Goodwin Aged Care Services is a registered charity operating retirement living, residential aged care, home care and allied health services.
Goodwin self-reported its non-compliance in July 2024, with the underpayments occurring between July 2018 and March 2025.
One employee is owed $38,760, while the average back payment for each employee was $4,165.
Most of Goodwin's affected staff were based in the ACT, according to the Fair Work Ombudsman (FWO), and included nurses, allied health professionals and care managers, along with staff in food, catering staff, cleaning, laundry and planning and admin staff.
For three quarters of those affected, English was their second language, and 10 per cent were visa holders.
"Migrants and visa holders are a priority for the FWO, as they can be vulnerable in the workplace including due to lack of awareness of laws or concerns about speaking up," Fair Work Ombudsman Anna Booth said.
She said the aged care sector was a large employer of migrant workers.
The FWO said Goodwin's non-compliance stemmed from sub-standard 'individual flexibility arrangements' (IFAs), which are alternative working terms made to suit both the employee and employer.
IFAs are required to leave staff "better off overall when compared to their award or registered agreement", the FWO said.
In 313 of these agreements, the FWO found the worker was disadvantaged due to the IFA being "over-reliant" on non-monetary benefits.
It also said due to an "incorrect payroll system configuration", 22 additional residential care employees not on IFAs had not been paid penalty rates for early afternoon shifts.
Goodwin is the latest aged care company to come from the FWO, after investigations earlier this year found 22 organisations owed more than $5.3 million to 3,600 employees.
The FWO said it is currently auditing 30 providers for compliance with the Fair Work Act.
Goodwin Aged Care said it has completed remediation for all affected employees it could contact, with funds for those it couldn't contact transferred to the FWO.
It also said it has worked to strengthen payroll governance and taken measures to prevent future similar issues.
"Goodwin acted promptly to understand their full extent and support affected employees," a spokesperson said.