"There is a new regime in town and things are going to be done different," Warren Mundine told NITV News.
"And the issue for us, into the new year, is to come out with those reform agendas that we need to do.
"I have had several good conversations with the government and also with the review board over the last week or so about looking at the economic growth, the economic development that needs to happen in Indigneous communities."
He says the had to be made because of the budget deficit revealed by Treasurer Joe Hockey earlier this week.
Treasurer Hockey says it's part of returning the national budget to good health.
Among the organisations hardest hit will be the National Aboriginal and Torres Strait Island Legal Services, or NATSILS.
"The government is in a fiscal, financial struggle with budgetary issues, Indigenous communities couldn't have been cocooned from that."
Future of National Congress of Australia's First Peoples in doubt
Meanwhile, the National Congress has been told to look for alternative funds as federal funding looks set to be stopped from July next year.
Indigenous Affairs Minister Nigel Scullion delivered the news directly to the Congress Co-Chairs.
"Given that the funding wasn't part of an election commitment, given the terrible economic circumstances that we've inherited, which was a reflection of MYEFO (Mid-year Economic Fiscal Outlook)...it was extremely unlikely they would receive their funding," Minister Scullion told NITV News.
Today, the National Congress was unable to comment on whether it is able to fund itself beyond July 2014.
"[We] will continue as a strong, fearless national representative body for Aboriginal and Torres Strait Islander Peoples," the body said in a statement.
Social Justice Commissioner Mick Gooda says the decision sends a poor message to the public on how much the federal government values Indigenous affairs.
"It's not a good look coming from the Prime Minister, who is supposed to be there for Indigenous affairs, when in the one week we see money removed from ALS's family prevention legal services - which is there to look after victims of domestic violence - and the abolition of the coordinator general's role, which was overseeing the coordination of efforts in remote Australia," Mr Gooda says. "On top of that this now happens."
Watch: Abbott government warns it will take the funding axe to National Congress, Lindy Kerin reports
