The Australian Heritage Commission has given the Federal Government the go-ahead to remove a burnt-out structure from the Aboriginal Tent Embassy in Canberra.

But a group of tent embassy supporters has filed an emergency declaration under the Aboriginal and Torres Straight Islander Heritage Act to protect the burnt-out shipping container.

Heritage Minister David Kemp must now decide whether the structure is of cultural significance.

The last-minute attempt to save the container comes after the Heritage Commission deemed the removal would not adversely affect the site, which is listed on the National Estate register.

The structure was badly damaged in a suspected arson attack more than a week ago and the Federal Territories Minister, Wilson Tuckey, has ordered its immediate removal.