The Northern Territory's corrections commissioner has revealed $64,000 was spent on a return charter flight to transfer 56 prisoners between Darwin and Alice Springs.

The measure was taken this week as the NT corrections department continues to respond to a surge in the NT's prison populations, which have hit a record capacity of 2,375 inmates.

On the weekend, Corrections Commissioner Matthew Varley said he was taking emergency steps to try and alleviate the pressure by transferring prisoners to different facilities across the NT.

Commissioner Varley was asked about the costs of transporting the prisoners, and cited the cost of a charter flight that saw 20 prisoners transferred to Alice Springs, and 36 to Darwin.

"I think the charter flight was about $64,000 return, but as I said, we moved 20 prisoners down and another 36 back.

"We did that in a space of about six hours, so it was a very efficient, economical, safe and secure way to do that transfer."

Legal service criticises prisoner transfer

Aboriginal legal service NAAJA has criticised the corrections department's move of taking Aboriginal prisoners to Darwin from their traditional country in Central Australia.

NAAJA's acting chief executive Anthony Beven said the transfer of prisoners from Darwin to Alice Springs and vice versa was "creating a significant disconnect for people".

"We're concerned about these transfers, and they seem to be based on overcrowding issues in the prisons and the remand centres, rather than what's in the best welfare of prisoners," Mr Beven said. 

"We're calling on the NT government to seriously re-look at these transfer arrangements, because they're going to lead to serious issues within jails, which is common when you've got issues around overcrowding and disconnect from their families and support services."

Commissioner Varley said the transfer needed to happen to free up police watch houses.

"Those were the decisions we took, and I stand by them," he said.

"The Corrections Act, the law, already allows me to transfer people around the entire network of Corrections.

"It's not unusual in large jurisdictions, large states, for correctional services to move people around prisons."

Fair Work lodgement against commissioner

Commissioner Varley on Tuesday also revealed the United Workers Union (UWU) had made a Fair Work Commission lodgement accusing him of breaching safe staffing levels.

"I will seek legal advice … and in due course I expect to have to front up to the Fair Work Commission and provide evidence and respond to those concerns," he said.

"What I have to focus on though is the operational circumstance in front of me, the work that my staff have to do in the trenches every day, and I'll deal with that when I get to it."

The prison population surge comes at a time of immense pressure on correctional officers, who are currently facing significant staff shortages.

Earlier in the week, the UWU's Erina Early said the emergency measures were putting the safety of prisons staff at risk including of a potential prison riot.

"There are really genuine concerns.

"We've got a lot of emotion here, we've got a lot of push to put more and more prisoners in there, but the thing that's being forgotten is we really don't have enough correctional officers to staff the safety of the prison."

Chief Minister Lia Finocchiaro was on Tuesday asked if she believed enough was being done to ensure the safety of staff and prisoners during the emergency period.

"I'm aware that there is a full plan in place," Ms Finocchiaro said.

"If there's a crisis, there's a plan. We're talking about a highly operational skilled environment, where risk is managed every day."

Commissioner Varley and Ms Finocchiaro have both said the opening of a new youth detention centre in Darwin next week would likely take some pressure off the prisons.