The case was filed after the department implemented the workplace determination set down by the Fair Work Commission, which said workers would only be paid for working at a higher level after doing so for 10 years in one financial year.

When the workplace determination was implemented earlier this year, the worker's acting EL2 salary was changed to her substantive EL1 salary for 10 days, even though she has been working at the higher level throughout the financial year.

The claim was for a small amount of money, $261.77, but the union saw it as a test case on an issue which was likely to affect others.

The union said court action should not have been needed.

"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 said.

"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."

A department spokesperson said where adjustments were needed, they would be made 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."