Up to 30 "critical" Border Force workers are considering leaving the Northern Territory after special salary allowances were cut this week, according to the Community and Public Sector Union.

Key points: Union claims that 30 Border Force workers have requested to leave the Territory after allowances were cut, and 150 NT workers would be affected

Union claims that 30 Border Force workers have requested to leave the Territory after allowances were cut, and 150 NT workers would be affected It says the remote living allowance is in place at a lot of agencies, and losing it results in a big pay cut

It says the remote living allowance is in place at a lot of agencies, and losing it results in a big pay cut CPSU has claimed some workers would be unable to afford rent due to the cuts

The CPSU said about 150 border force workers who manned customs stations on the Top End border have not seen a pay rise since 2013.

Now, this latest move from the Home Affairs Department will see a removal in a remote living allowance for Darwin workers.

The union claimed customs workers in the Territory would potentially be paid $5,000 less than they were receiving five years ago.

CPSU NT secretary Kay Densley said the move would severely affect staffing on borders in the Top End.

"The NT needs people," she said.

"We can't afford to lose people and the whole thing stinks really."

Long-term wage cuts on cards

Ms Densley added that a further $1,700 dollars in wage cuts would be phased in over the next two years.

"So when you have experienced and trained people who are the ones checking people, checking freight, we need people who know what they're doing, they're critical," she said.

"And they're not being treated with respect."

Ms Densley claims the Home Affairs Department had "robbed" the workers and said many of them would not be able to afford rent and could go into debt.

"When you're getting paid $5,000 less than you were in 2013, you have to think twice about what you're going to do, and they're thinking about leaving," she said.

"The remote living allowance is to cover the cost of living in the Northern Territory — that happens at a lot of agencies and it's a big cut to people's pay and they don't deserve it."

The union is now handing out a petition of workers stating "no confidence" in the Home Affairs Department secretary Michael Pezzullo and Minister Peter Dutton.

"This document will be collecting signatures from all our Home Affairs staff and our members," Ms Densley said.

"We'll be presenting this to Scott Morrison and Bill Shorten and asking them to step in and restore the wages and respect for our staff."

Home Affairs Department refutes claims

A Home Affairs Department spokesperson rejected claims that it had effected a pay freeze and said it had been negotiating in good faith with the union to deliver a pay rise across the workforce.

"We reject assertions from the CPSU that the Department has effected a wage freeze," the spokesperson said.

"The CPSU actively campaigned against the Department's three offers, the last of which would have delivered pay rises of up to 10.4 per cent from 2016."

The Department also refuted the claim that Border Force workers had voiced their plans to leave the NT.

"There have not been mass requests for transfers from Australian Border Force officers," the spokesperson said.