According to the Community and Public Sector Union, pay rises beyond the 2 per cent annual cap in the government's policy is a win, as is the retention of allowances for use of force by Australian Border Force officers, dog detector unit handing allowances and training officer allowances.

The department and the union had been locked in negotiations for three years, each failing to cede ground until the case was heard by the full bench of the Fair Work Commission, with hearings beginning in 2017, closing in 2018 and finally resolved with the determination handed down last week, five years after the last agreement was set to expire.

Also counted as wins was the retention of the national staff consultative forum, other consultation requirements and performances management categories, as well as the requirement that overtime be paid after a standard work day.

The union considers a longer working day for Border Force employees among the negatives, as well as five days extra work per year for members of the Marine Unit. The loss of allowances for those working at airports and other location-based allowances also counted in the negative category.

"This decision is far from a perfect outcome but shows, when workers are faced with the choice of the scorched earth approach taken by the Government and department or fighting to protect their conditions and pay, this was a fight worth having," Community and Public Sector Union national secretary Nadine Flood said.

"We’ve been able to hold onto some allowances and conditions and secure a pay rise beyond the Government’s low wage cap, including some backpay. We are disappointed with many elements of this determination, but recognise that Fair Work’s options have been limited by a system that is broken and needs to be fixed."

The Fair Work Commission deferred many issues in dispute to further rounds of bargaining, with the determination set to expire in two years.