The head of the Prime Minister's Indigenous Advisory Council, Warren Mundine, has warned his fellow councillors to be prepared to be among the most hated people in Australia after next month's federal budget.

Mr Mundine has told the ABC he expects there will be cuts to Indigenous funding in the budget as the number of program areas is reduced from about 150 to five as part of a "realignment" of spending.

The five key program areas identified by Mr Mundine are: health, education, jobs, law and sustainable communities.

It is not clear what this will mean for dedicated Indigenous service providers across the country but some organisations are worried they will be forced to cut staff.

Mr Mundine has backed cuts to get rid of duplication, but says he expects people from a number of Indigenous organisations and programs will be unhappy.

"In fact I said to the council at their first meeting, 'be prepared after the May budget in 2014 to be the most hated people in Australia'," he said.

Canberra's Winnunga Nimmityjah Aboriginal Health Service is one of the medical services that could lose funding as part of the changes.

Stolen Generations member Lisa Chatfield describes Winnunga as her life saver.

"[It] got me back on my feet, I'm a reformed alcoholic and a reformed drug abuser," she said.

"There's no other place to go here in Canberra who understands where we're coming from and the cultural differences."

The Federal Government has told Aboriginal medical centres across the country that core funding for general practice services is safe for the next 12 months.

Despite the assurance, Winnunga chief executive Julie Tongs is worried services that rely on additional funding could be cut.

She says she will lose 11 Aboriginal staff members if that additional funding does not come through.

Program area cuts will focus help for Indigenous: Mundine

In 2012, a Council Of Australian Governments (COAG) report estimated total Indigenous expenditure by all levels of government was more than $25 billion.

Mr Mundine does not know what impact next month's budget will have on that figure but he is expecting a number of program areas will be cut.

"The idea is to reduce the number from about 150 right back to about five in the program areas so that we're focused, so that we are hitting the right targets that are going to deliver the outcomes to close the gap," he said.

Opposition Indigenous affairs spokesman Shayne Neumann says he is worried about duplication being used as an excuse to cut national partnership agreement funding from the states and territories.

"If those type of partnership agreements are not proceeded with then the states and territories don't have to put up a dollar towards those things and we'll see a cutback, not just from the Federal Government point of view, but from the state government and territory government point of view," he said.

Ms Tongs is more confident than Mr Neumann, but will read the budget as a test of Prime Minister Tony Abbott's promise to be the prime minister for Indigenous affairs.

"I know Tony Abbott, Tony Abbott's been here a few times when he was the health minister and also the opposition leader and I'm quietly confident that we will survive whatever comes," she said.

If you have more information, please email: investigations@abc.net.au