The Victorian Opposition is calling for an investigation into the loss of Aboriginal human remains from the Melbourne Museum.

The remains were lost in 2001 when the museum relocated to Carlton.

Freedom of information (FOI) documents have revealed that the museum does not know if the remains were simply misplaced or stolen.

Victorian Opposition spokesman for the arts, Andrew Olexander, says the State Government has known the remains were missing since 2001.

"[Victorian Minister for the Arts] Mary Delahunty has known for three years that these significant human remains have been missing from [the] Museum of Victoria and for three years nothing has been said to Victoria's Indigenous community about the loss," Mr Olexander said.