The YiSSA short-stay accommodation centre in Darwin was set to close its doors on Monday on the orders of the Northern Territory government.
The centre has held up to 400 mainly Aboriginal residents, including domestic violence survivors and people from remote communities who need access to life-saving medical treatment such as kidney dialysis.
The NT government planned to bus residents who hadn't found alternative accommodation to demountables in the township of Batchelor, 100km south of Darwin.
YiSSA resident Tilathia Gore, 38, told AAP outside the centre on Monday she had no choice but to take the bus to Batchelor.
"We're getting shipped out against our own will and we're hearing the facility out there is not even done up properly.
"We've got kids, old ladies coming out with us, if anyone gets sick it's going to take forever for an ambulance to get out there," Ms Gore said.
"It's sad, it's heartbreaking, we've got everything here in Darwin for us. Going out there, it's going to be hard."
The NT government decided to close the shelter despite the federal government offering to pay $3.5 million towards a shared-purchase arrangement to keep it open.
Federal Minister for Aboriginal Australians, Malarndirri McCarthy, said last week there were more than 120 people in the facility who had not found anywhere to go.
She urged the NT government to extend the centre's life for at least six months, to beyond the wet season, so a long-term plan could be worked out for vulnerable families.
Batchelor resident Maemae Morrison told AAP her community lacked the services and amenities to cope with an influx of vulnerable people.
Children and Families Minister Robyn Cahill told reporters NT Health was working to find accommodation for YiSSA dialysis patients close to services in Darwin.
NT Opposition Leader Selina Uibo said the NT government had botched the relocation, with questions remaining over whether contractor Mission Australia had enough staff to provide 24-hour support at Batchelor.
There were also questions over how residents would be supported to travel 100km back to Darwin for medical appointments and work, she said in a statement.
"There are also 53 school-aged children whose education needs to be considered. How many will attend Batchelor Area School, and what extra teachers and support will be available?"
On Monday one bus was scheduled to do a pick-up after the centre's children returned from school, with them expected to start school in Batchelor on Tuesday.
The NT government should abandon the relocation and allow the YiSSA centre to remain open, Ms Uibo said.
NT Chief Minister Lia Finocchiaro has defended the relocation.
"We have stood up an alternative facility that provides people food, care, clothing, a warm bed, a roof over their head," she said.
Last Tuesday about 300 people protested against the YiSSA centre's closure outside a homelessness conference at the Darwin Convention Centre.
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