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The Museum advises on and assists federal, state and territory cultural heritage institutions, Indigenous communities and representatives with the repatriation of Indigenous human remains and secret/sacred objects. It also provides information to the media and general public about repatriation.

The management of human remains and secret/sacred objects is strictly controlled by the Museum's Repatriation section to ensure that material is cared for in a culturally sensitive and appropriate manner, as well as in accordance with museum best practice.

The Museum has not actively sought to acquire human remains or secret/sacred objects.

However, as the prescribed authority under the Aboriginal and Torres Strait Islander Heritage Protection Act 1984, the Museum can be the repository for unprovenanced remains referred to the Australian Government minister under the Act. To date, no remains have been deposited with the Museum under this Act.

The Museum also holds human remains and secret/sacred objects transferred from the Australian Institute of Anatomy collections in 1985. These have been de-accessioned and do not form part of the National Historical Collection.

During 2008–09, the Museum transferred the remains of 14 individuals to the Kimberley Aboriginal Law and Culture Centre in Fitzroy Crossing.

The Museum also holds repatriated remains at the request of a number of communities, and is funded by the Department of Families, Housing, Community Services and Indigenous Affairs to assist in the storage and repatriation of remains and objects returned from overseas collections.

In 2008–09 the Museum helped the Seattle Art Museum in the repatriation of a secret/sacred ceremonial stone to Australia. This is the first time an American cultural institution has initiated the return of a secret/sacred object to an Australian cultural institution. The Museum took delivery of the stone, which had been in the Seattle Art Museum's collections since 1971, in June 2009. The stone will be housed in a restricted store while the Museum consults with Central Australian elders and their representatives to determine the culturally appropriate management and return of the stone.

Repatriation activities during 2008–09 were primarily supported by Museum resources. Funding was also provided through the Return of Indigenous Cultural Property Program, an initiative of the Cultural Ministers Council and administered by the Department of the Environment, Water, Heritage and the Arts.