The head of a Senate committee into the abolition of ATSIC has expressed doubt the Federal Government will listen to the outcomes of the inquiry.

Committee chairwoman, Northern Territory Labor Senator Trish Crossin, says the majority of the more than 200 submissions received so far have rejected the Federal Government's plans to transfer the administration of Aboriginal affairs from ATSIC and ATSIS to its departments.

Senator Crossin says Indigenous people want to be consulted, but she is worried they may miss out on that opportunity.

"I'm hoping the Government does listen to this because how are they ever going to determine how the bureaucrats, in the coordinating centres, spend their money, who they consult with and what the programs are going to be," she said.

"There is a layer in this legislation that has been stripped away and Indigenous people are saying to us loud and clear that's what they want put back on the table."