More than 300 vulnerable people, including almost 90 children, who are currently waiting for support in the Northern Territory will need to find alternative accommodation after the government ordered a homelessness service to stop accepting new check-ins.

Earlier this month, it was reported the Country Liberal Party (CLP) Government had given Yilli Rreung Housing Aboriginal Corporation 90 days to vacate its short-stay accommodation premises.

Currently, 223 adults and 136 children live at the YiSSA shelter on Batten Road in Marrara, many from remote communities, with no certainty that current occupants will have somewhere to go.

Under the direction of the Department of Children and Families, people staying in the 28-day accommodation program will be required to leave by 25 August, while all remaining residents are expected to vacate the site by 11 October.

Current system cannot absorb demand

In a joint statement, Yilli Housing Aboriginal Corporation, Mission Australia, Aboriginal Housing NT and NT Shelter said the Department had instructed Yilli Housing to stop accepting new check-ins to YiSSA's 14-day and 28-day accommodation programs from Monday.

"The decision means more than 300 people currently waiting for support, including 89 children, will need alternative pathways as the Territory's largest homelessness accommodation service closes," they said.

Yilli Housing Aboriginal Corporation chief executive officer Yvette Park said the transition had begun.

"People are facing uncertainty about where they will go next," she said. "Families with children are feeling the impact, and staff are working hard to support residents through a difficult transition."

The Northern Territory has the highest rate of homelessness in the country, almost 12 times the national average. Aboriginal and Torres Strait Islander people comprise 87 per cent of the Territory's homeless population.

Aboriginal Housing NT chief executive officer Leeanne Caton said many vulnerable people in the Territory relied on YiSSA to provide a "safe place to stay while accessing medical care, escaping violence, connecting with services or taking steps towards stable housing".

"For many families from remote communities, Aboriginal community-controlled organisations must be genuine partners in planning the next steps for families," she said.

The Territory has an extreme housing shortage, with social housing wait times exceeding ten years in some areas. Homelessness services are already operating at capacity, the groups said.

"When housing and accommodation options are limited, pressure is felt across families, communities and already stretched services," NT Shelter chief executive officer Annie Taylor said.

Detailed transition plan needed

The property sits on Crown land, while the buildings are owned by Ausco and leased to the Northern Territory Government under a five-year agreement worth between $2.5 million and $3 million per year.

Child Protection Minister Robyn Cahill previously said Ausco "would not come to the party," despite the government offering a "fair market price in an effort to be able to continue to function at that site". However, the NT News reported at the weekend the government had offered Ausco $3 million to purchase the property.

The owners value the entire 300-room facility at between $8 million and $12 million, having previously spent $25 million developing the 7.5-hectare site in 2012.

Ms Cahill has said there is a transition plan in place. However, more than two weeks after the announcement, no details have been made public.

"We share Minister Cahill's objective that nobody will be on the street as a result of YiSSA's closure," Mission Australia's Sue Budalich said. "A clear transition plan with clear accommodation or housing pathways will be critical to achieving that outcome."

The four organisations said they acknowledged the government's intentions and commitment to work with providers, but more certainty was needed.

"A strong transition plan should identify safe and appropriate housing pathways for every resident, contingency arrangements where housing is unavailable, and tailored support for families with children and people with complex needs," Ms Park said.

"Alternative options must also be scaled up to support the thousands of people assisted each year and replace YiSSA's 200 rooms. We remain committed to working constructively with Government to protect vulnerable Territorians and develop a workable solution."