Home Affairs has paid an employee on the same day her underpayment case was lodged in the Federal Court.

The Community and Public Sector Union (CPSU) lodged the Federal Court case on behalf of the worker.

The case came after a Fair Work Commission finding that workers would only be paid for working at a higher level after doing so for 10 days in one financial year.

When the determination was implemented, the worker's acting EL2 salary was changed to an EL1 salary for 10 days, even though she had been working at the higher level earlier in the financial year.

She was short-changed just $261.77, but the union said it needed a test case on the issue.

“There should have been an apology alongside this payment to acknowledge the unnecessary rigmarole our member has been put through,” Community and Public Sector Union deputy national president Lisa Newman has told Fairfax.

“We are concerned that the higher duties clauses aren't the only part of the Workplace Determination that Home Affairs is not implementing correctly. The department needs to work cooperatively with the union to ensure that workers receive the pay and entitlements that Home Affairs are legally obliged to provide.”

The department corrected the payout almost immediately, saying that it makes such adjustments as quickly as possible.

“The department will make payments to all staff in accordance with the terms of the workplace determination and supporting policies; which are being developed through a process of consultation and engagement,” Home Affairs said in a statement.