ATSIC Central Zone Commissioner Alison Anderson says the Federal Government should reveal where it is storing Aboriginal art works that were taken from the commission's offices over the weekend.

Ms Anderson is angry she was not told the art works were being removed from her office in Alice Springs in central Australia yesterday.

Aboriginal and Torres Strait Islander Commission transferred the ownership of millions of dollars in property to individual communities on the weekend and says it made the decision to stop its assets going into Federal Government coffers.

The Government seized ATSIC's art collection and stored it at an undisclosed location.

She says the Government should be more transparent about the process.

"I want to know where these paintings are and how they're being treated because they carry a lot of history and it's like thieves in the night, they come in and take things out of peoples' offices," she said.

A spokesman for the Indigenous Affairs Minister, Senator Amanda Vanstone, says the Commonwealth will ensure ATSIC's property is available for the benefit of the Indigenous community.

The Federal Opposition says the ATSIC decision to transfer its assets to Aboriginal groups around Australia is legitimate and should be allowed to go ahead.

Labor spokesman on Indigenous affairs, Senator Kim Carr, says he is concerned about the way ATSIC's actions have been portrayed.

"What concerns me is the innuendo and the aspersion that people are being acting in an illegal, improper way, when there is no evidence put forward," Senator Carr said.