The Community and Public Sector Union will leave unchanged its primary position on wages and conditions, but as the case reaches closing arguments it will offer the Full Bench of the Fair Work Commission an alternative should it decide not to accept either party's arguments in full.

Under the alternative position, the union would agree to treat some of the conditions of staff at the former Australian Customs and Border Protection Service separately from those in the former Immigration Department.

“Our position on the key elements of this dispute remains absolutely unchanged," the CPSU said.

"That means we remain resolute in demanding these workers retain their existing workplace rights and conditions and get a decent pay rise that acknowledges the long hard road these members have travelled just to get some basic respect from their bosses and the Turnbull government."

The fight over a new workplace deal has been complicated by the 2015 merger between Customs and Immigration, leaving public servants trying to negotiate a single workplace agreement under the Coalition's strict bargaining rules.

Union lawyers have advised the CPSU to simplify Fair Work's decision as the bitter fight over a new enterprise agreement dragged well into its fourth year and the industrial umpire faced arbitrating a matter fought across multiple fronts.

"This will minimise the risk of a lengthy deliberation that could result in an outcome that impacts on the workers who stand to lose the most,” the CPSU said.

Home Affairs appeared to swipe at its decision in a statement on Friday, saying each party was given since November 2016 to prepare and submit its positions and that the department had left its own largely unchanged.

"On 12 April 2018, with only two working days to go before the final hearings commence, the CPSU announced to its members that it intends to put an alternative proposal to the Full Bench for their consideration. One that has not been addressed in the significant time already spent on this matter," it said.

Home Affairs - created in another merger involving the former Immigration department in December - said it warned staff a Fair Work arbitration could be lengthy.

Fair Work will arbitrate the pay and conditions of workers in what has been described as the largest industrial relations case since Qantas grounded its aircraft in a high profile workplace dispute six years ago.

It began hearings in October more than a year after it halted industrial action by union members including strikes at Australia's international airports, and staff have gone without a pay rise in more than four years.

Lawyers for Home Affairs have told the Full Bench of the commission that the department's offer to staff balanced competing interests and provided flexibility while the proposed pay rise took account of economic conditions.

The CPSU later said the then-Immigration department had ignored workers, would not negotiate changes to its offers, and had adhered too strictly to the Coalition's public service bargaining rules.

Home Affairs and the CPSU will make final submissions to the commission on Monday and Tuesday.