Aboriginal organisations in the Northern Territory are beginning to realise the full cost of funding cuts under the Federal Government's Indigenous Advancement Strategy (IAS), and have called on Indigenous Affairs Minister Nigel Scullion to be sacked.

Peak Aboriginal organisations from Central Australia held an emergency meeting in Alice Springs on Tuesday to discuss expected cuts to frontline services following the announcement last week of who will share in $860 million of Commonwealth funding.

Some of the groups have said they would put off staff and cease services to remote communities in the coming months.

Institute for Aboriginal Development (IAD) chief executive Jenny Bedford said the organisations wanted Mr Scullion dumped as Indigenous Affairs Minister.

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"The fact that we have got language that is sort of indicating and saying to us that we are a hopeless bunch of organisations, coupled with the fact that there has been significant cuts to Aboriginal organisations, is quite an alarming thing for our communities," Ms Bedford told 783 ABC Alice Springs.

"We have made a strong stance on that and we are calling on the Prime Minister to stand the Minister down," she said.

MacDonnell Regional Council president Sid Anderson attacked the Prime Minister yesterday, saying his council would have to sack 51 Aboriginal people as a result of cuts delivered via the IAS.

Mr Andersen said jobs run by the council on community night patrols and in early childcare programs would have to go.

He said MacDonnell Regional Council had been asked to expand its frontline services in remote Aboriginal communities despite a cut to its budget through the IAS of more than 30 per cent.

Mr Anderson described the budget measures as a direct attack on the wellbeing of Aboriginal people living in remote areas.

Fellow councillor Greg Sharman is concerned anti-suicide and substance abuse programs could be threatened by the funding cuts.

"These are the people who are working with our kids, that are working with our future," Mr Sharman said.

"If they're not getting any guidance they're not going to go in the right direction.

"We've got people out here doing programs about not doing suicide, staying away from drugs, staying away from alcohol.

"If they're not being told that sort of stuff they're going to be led astray."

Cuts to youth services

Wendy Morton is the CEO of the Northern Territory Council of Social Services. Her members include NGO and not-for-profit organisations.

Ms Morton said there was widespread confusion over who the winners and losers in the AIS grants are.

She said some organisations had received a portion of the money they asked for while others had lost out altogether.

"What I'm hearing anecdotally is that programs primarily working with young people have been hit," Ms Morton said.

Executive Director at the Northern Territory Council of Social Service, Wendy Morton. ( Supplied )

"We've heard stories like this from Tennant Creek, Alice Springs and Darwin."

Ms Morton said the social services sector in the Northern Territory was more uncertain than it had been in a decade.

"Certainly it's pretty frustrating and heartbreaking, particularly when you're working with people on the frontline," she said.

"Working with people who are at risk and you know that if those services aren't delivered we'll have more children in our detention centres.

"We'll have more people in our hospitals. We'll have less children going to school, less people in employment."

Most service providers the ABC has contacted have declined to comment on their funding for fear of losing future financial support from the Government.

Central Australian Aboriginal Legal Service suffered 'significant blow'

The Central Australian Aboriginal Legal Service (CAALAS) said the future of its youth justice advocacy program had suffered "a significant blow".

The advocacy project works with young offenders in the Alice Springs criminal justice system, almost all of whom are Aboriginal.

CAALAS principal legal officer Mark O'Reilly said the program was not given enough money from the Federal Indigenous Advancement Strategy to fund its single staff position.

"We got a letter saying that we were successful [but] it was really only a partial success and it leaves us in a quandary really," he said.

"The amount of money fell way short of what we were asking for and its certainly not enough to run the program as it was put up."

Darwin loses volatile substance program

The CEO of Amity, which provides counselling services for people with drug and gambling problems said his organisation would lose four staff and the ability to deliver frontline services to 300 people.

"We previously had received funding for working in the town communities on the abuse of volatile substances, but we've been advised that we've been unsuccessful," Bernard Dwyer said.

Mr Dwyer said the program Amity would have to close targeted sniffing and other substance abuse amongst young people, as well as drug and alcohol issues in the adult population.

Amity had asked for $480,000 in funding from the Indigenous Advancement Strategy but was not granted any of that money.

Western Australia - no rangers down south

The Goldfields Land and Sea Council (GLSC), which provides services to Aboriginal people in an area stretching from Laverton to Esperance and east to the coastal border of South Australia, did not receive any of the $3 million it requested through the IAS.

Rangers and ranger coordinators at Credo Stations in WA's Goldfields.

Darren Forster from the GLSC, said the council wanted to fund an Aboriginal rangers program.

Mr Forster attended a community event in Kalgoorlie with the Prime Minister on Tuesday but was unable to ask Mr Abbott why the Goldfield Sea and Land Council missed out on federal funding for rangers.

"The north [of WA] gets funded, the south doesn't," Mr Forster said.

He claims while "billions of dollars" of Commonwealth money go north to Aboriginal programs in the Kimberly, he was not aware of a single Aboriginal ranger position supported by the Commonwealth in the southern half of the state.

"We don't begrudge the northern mobs. We think what they're doing is great. But the money should be more equitably spread," he said.

Response from Minister Scullion

In a statement, Mr Scullion said the Government had committed to a $4.9 billion investment over four years in the IAS.

"The Government will invest more than $860 million under the current IAS grant funding round to deliver on its key priorities of getting children to school, adults into work and ensuring communities are safe," the statement said.

"Every effort has been made to ensure effective frontline services that deliver on outcomes are maintained. We have also been mindful to support Indigenous organisations and support Indigenous employment."