Lodged by the Community and Public Sector Union on behalf of a staff member acting at EL2 level, the case rests on when a staff member should be paid a higher duties allowance.

After the Fair Work Commission handed down a workplace determination governing pay and conditions at the department in February, the department has been working to update its practices.

The new determination says where an employee works at a higher level, the allowance will be paid after they have worked at that level for 10 days.

If they have already worked at a higher level for 10 days in a financial year, "all subsequent periods of acting will attract a higher duties allowance from the commencement of the period of acting".

According to the union, the staff member went from being paid as an EL2, to 10 days paid as EL1 at the start of the workplace determination, despite having already been acting at a higher level throughout the financial year.

The small claims application covers a small amount of money, $261.77, but it's believed the issue likely affects many other staff members.

"Home Affairs has a huge in-house legal team on top of the army of lawyers they engaged during the Fair Work arbitration process, and yet the department still doesn't seem to understand how to properly apply the Workplace Determination that resulted from that long, drawn out process," union deputy national president Lisa Newman said.

"Home Affairs workers who take on higher duties have a legal right to be paid in accordance with the Workplace Determination. The department has failed to do that in this case, and in many other similar instances that we're currently investigating. Higher duties allowances are just one of the areas where we believe Home Affairs is underpaying staff."

A Home Affairs spokesperson said the department didn't comment on individual matters.

"The department is currently in the process of implementing the workplace determination," the statement said.

This includes methodically working through clauses, sharing our views on supporting policies and procedures with our staff and seeking their feedback. This is important to us. We have, and will continue to, refine supporting policies and procedures based on input from our staff."

The workplace determination was made by the Fair Work Commission after negotiations between the department and the union broke down after years of fighting.

A complicating factor in the case was the merging of former Customs staff with Immigration staff in what was then known as the Department of Immigration and Border Protection.

The department was also limited in what it could offer by the government's workplace bargaining policy.

Customs staff, which include those working in airports, harbours and off-shore, generally had more generous allowances than their colleagues from Immigration.

Staff members have already said they are concerned by the security implications of new allowances for those working in remote areas, many of whom will receive less in allowances under the new system.

They worry that if experienced staff decide they can't afford to work in remote locations, those ports could become vulnerable to drug and people smuggling operations.