The Darwin Aboriginal and Torres Strait Islander Women's Shelter has been informed funding for its emergency relief programs will cease at the end of this year.

And Katherine's only refuge for women escaping domestic violence will see the same fate if the government continues on its path.

NT Labor Senator Malarndirri McCarthy is today calling on the Morrison Government to reinstate critical emergency relief funding.

With no alternatives for Katherine women, she said the homelessness crisis gripping the town will only worsen.

"I know the Katherine Women's Crisis Centre gets calls at 3am from women at the hospital who need help getting to the shelter.

"We are not talking millions here, we are talking in simple terms of money that provide people with food coupons, vouchers for taxis, accommodation for the night if the centre is at capacity.

"I do not want to see these families on the street adding to the homelessness that is already such an issue in Katherine."

Emergency relief funding provides essential support to women and children by helping them relocate from unstable or dangerous households, ensuring they have access to essential items such as food, as well as case management services.

In the past three months an average of 60 women and children sought out the crisis centre's help with Indigenous women at particular risk.

"My concern is that more than 90 per cent of the women who access the service are First Nations people," Ms McCarthy said.

"The Women's Crisis Centre is terrific in cultural competency... it is amazing at dealing with women from across the region, but once governments start telling them they have to go to main stream organisations, that widens the gap."

The Katherine Women's Crisis Centre has been hanging on by a string since the beginning of this year, and it is not the first time fears for the centre have been raised.

In the lead up to the federal election in May of this year, Ms McCarthy was joined by Labor Senator Jenny McAllister and veteran Labor MP Warren Snowdon with a promise of funding if successful - even then the service was facing the harsh reality it would be forced to turn people away by year end.

The Darwin Aboriginal and Torres Strait Islander Women's Shelter was informed on September 30 it would need to direct its clients to mainstream services.

But the manager of DAIWS Regina Bennett says with only one other Indigenous-run service available to women in Darwin, the move would be "bedlam".

"I'm really worried about our clients," she said, "we've been told to transition clients to other organisations. Only one of those organisations is Aboriginal-operated.

"The program has been very critical for our clients, and to lose it and have to seek assistance from the mainstream organisations is very demeaning, insulting, and time wasting."

DAIWS provides two 24-hour Domestic Violence Crisis accommodation centres for women and children escaping domestic, family violence, and sexual abuse and assault. It also provides eight transitional housing units and domestic violence outreach programs for women and children.

"I was under the impression that as part of closing the gap for Aboriginal people, that Aboriginal organisations would be considered as the best placed service, which provides culturally appropriate programs to our vulnerable families," Ms Bennett said.

"If we lose the emergency relief program, this is going to widen the gap, instead of closing the gap for our Aboriginal families in crisis."

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