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Agencies wait to hear fate as Indigenous Advancement Strategy grants list is finalised

A frontline organisation dealing with domestic violence in the Northern Territory says its funding has been cut in half.

It comes amid general uncertainty about the fate of funding applications as hundreds of other agencies wait to hear whether they have received much-anticipated Federal Government money.

In what it claimed was a "completely separate" development, the Department of Health has also made a separate funding announcement of $1.4 billion over three years to Aboriginal community-controlled health organisations.

On Wednesday, Canberra announced the number of organisations set to share $860 million in grants under the new Indigenous Advancement Strategy (IAS).

The new strategy, consolidating more than 150 programs, grants and activities, was announced in the federal budget in May 2014 and will see $534 million cut from Indigenous programs administered by the Prime Minister and Cabinet and Health portfolios.

Since last year, agencies have been waiting to hear if their grant applications have been successful.

The National Aboriginal Community Controlled Health Organisation (NACCHO) said the result had caused confusion among its members.

"Their concerns are being raised with me every hour of the day since the announcement was made by Minister Scullion," NACCHO Chairman Matthew Cooke said.

The ABC has contacted dozens of groups who applied for funding under the IAS.

A handful received positive letters on Thursday, but later learned that success did not mean they had received all the money they had requested.

Service providers said the AIS process has been chaotic since it began 12 months ago.

Estimates on Friday heard more than 2,300 organisations applied for funding.

Of those, 964 have been awarded grants.

Katherine Women's Information and Legal Service chief executive Sandra Nelson said the 50 per cent cut to its budget would mean "a reduction in access to justice for Indigenous women".

"We employ four people so two people will have to go," she said.

In Federal Parliament, Labor Senator Nova Peris asked Minister for Indigenous Affairs Nigel Scullion if he stood by his claim the Government's decision to cut $500m from Indigenous funding would not have an impact on frontline services.

"All of the family violence centres have been funded to the exact same extent as they were," Senator Scullion said.

"There are some who applied separately for different funds.

"In some cases [they might have received] substantially less than what they applied for in the separate funding."

On Wednesday, Greens Senator Rachel Siewert described the Indigenous Advancement Strategy grant announcement as a "mess".

"The Government's cut from the program over half a billion dollars, so there are going to be some organisations who when they finally get through find out they have not been funded," she said.