There are fears hundreds of vulnerable people in the Northern Territory will be at risk of homelessness after the shock closure of an Aboriginal corporation's shelter.

On Tuesday, NT News reported the NT Government had given Yilli Rreung Housing Aboriginal Corporation 90 days to vacate its short-stay accommodation premises, with an internal email from YRHAC chair Regina Bennett, cited by the publication, calling it "very concerning news".

Currently, there are 230 adults and 160 children — many from remote communities — at the shelter on Batten Road in Marrara. Currently, there is no certainty any of them will have a place to go.

Opposition Leader Selena Uibo said the NT Government's decision had been made "with no clear plan for thousands of Territorians who rely on it each year".

"These are families travelling in from remote communities for medical treatment and to access other essential services who will now be left without accommodation when they come to Darwin," she said.

It was reported the "short-sighted decision" to close the shelter would also impact 25 staff.

Children and Families Minister Robin Cahill said a transition plan was in place, telling reporters on Wednesday the government "offered a fair market price in an effort to be able to continue to function at that site" to the owners of the facility's infrastructure, but it was rejected.

"Let's just say that their response was far from fair and far from conducive to a good, smart economic decision, so we will have to transition those people out," she said, the NT News reports.

"We're not reducing services; it will simply be a realigning of services to other areas."

Ms Uibo claimed the Minister's priorities were "completely backwards".

"Her first responsibility should be making sure vulnerable Territorians have somewhere safe to stay, not closing the accommodation they rely on with no alternative in place," the opposition leader said.

"In the same week she announced another homelessness advisory group, she is overseeing the closure of one of Darwin's largest accommodation providers for people who desperately need support."

The NT has the highest rate of homelessness in Australia, at about 12 times the national average. Indigenous people comprise 87 per cent of the homeless population in the Territory.

Delivering the keynote address to the Aboriginal Housing and Homelands Conference in Darwin in May, independent senator Lidia Thorpe accused the NT Government of racism and launching a "direct assault" on First Nations people with its policies.

She argued inadequate, overcrowded, unsafe and insecure housing was at the root of many of the problems Indigenous people were experiencing.

"It leads to preventable disease, lower life expectancy, higher absentee levels in schools and limited job opportunities, just to name a few," she said.

"It intentionally leads to further criminalisation and more child removals."