Indigenous Affairs Minister Amanda Vanstone has hit out at Aboriginal and Torres Strait Islander Commission (ATSIC) commissioner Ray Robinson over his support for Labor's plan to abolish the peak Indigenous body and its related agency the Aboriginal and Torres Strait Islander Studies Unit (ATSIS).

Senator Amanda Vanstone has told the Senate that a recent ATSIS audit of eight companies associated with Mr Robinson, which have received government grants, found that $1.9 million remains unaccounted for.

Senator Vanstone says Mr Robinson supports Labor's policy because he is opposed to financial accountability.

"Now what Mr Robinson is doing is in effect saying just give the $1 billion spent on Indigenous welfare annually by ATSIC or ATSIS now to organisations such as the one he controls and ask no questions," she told Parliament.

"Clearly Mr Robinson sees the prospect of returning to a system where he can escape scrutiny and we will not endorse that."