Children are set to be moved out of Darwin's Don Dale Youth Detention Centre for the final time, as an overburdened Northern Territory jail system continues to play musical beds with prisoners.

The NT Department of Corrections on Saturday implemented emergency measures in response to a rapid and continuing surge in prisoner numbers across correctional facilities and watch houses.

As part of Correction Commissioner Matthew Varley's plans to reduce overcrowding, children at Don Dale will be moved into a new purpose-built facility next to the adult corrections centre in Darwin.

Corrections staff were "on track" to open on Monday, Mr Varley said, as they made final preparations at the new Holtze Youth Detention Centre.

The move will free up 50 beds for low-security men housed at Berrimah.

"The cards that were dealt every day by the courts, police activity and community safety and crime issues are the cards we're dealt... I'm just focused on responding to that," he said.

"I think we're a few weeks away from establishing that Berrimah men's facility, as soon as the young people move out, we will be turbo charging those infrastructure works."

Aboriginal and Torres Strait Islander young people aged 14-17 are incarcerated at a higher rate in the NT than anywhere else in the country.

Last week it was revealed part of the new prison expansion will see children transported from Central Australia to Darwin to be housed 1500 km away from their family and culture.

The Northern Territory children's commissioner, Shahleena Musk, said she was "deeply concerned" by the announcement.

"Whilst they may have been deprived of their liberty, these children still have the right to be connected to their culture, their loved ones and their community," Commissioner Musk, a Larrakia woman and former crown prosecutor, said.

The territory's three specialist women legal services said they also had grave concerns for women transferred from Alice Springs to Darwin.

Katherine Women's Information and Legal Services chief executive Siobhan Mackay said more than 40 women had been moved since Sunday.

"The earliest (corrections) could book us to speak with our clients is Friday," she said.

Transferring women 1500 kilometres has severe consequences, the Central Australian, Katherine and Top End women's legal services said in a joint statement.

They said women were bearing the brunt of the "overburdened justice system" and moving them was a breach of international human rights, severing connections to their children, culture, community and country.

More than 100 more prisoners have entered the system since the Country Liberal Party was elected in August.

Chief Minister Lia Finocchiaro said stronger bail laws passed by parliament would be implemented by January to allow adequate time for necessary operational changes in the justice system, and Corrections.

United Workers Union secretary Erina Early said she was having productive discussions with executives at both prisons regarding the safety of staff and operations.

The discussions had progressed because they were with people "who work behind the wire" and understand the need for "staff safety" Ms Early said.

Earlier, 700 workers pledged to strike if conditions were not resolved.

The government said corrections staff had been placed in a difficult situation, bearing the brunt of years of neglect of the system.

(A)manda Parkinson - AAP