Controversial legislation to excise the Australian mainland from the migration zone to deter asylum seeker boat arrivals has passed parliament.

Federal Labor, with the backing of the coalition, on Thursday successfully steered its excision legislation through the Senate and the lower house - a move labelled by the Australian Greens as a stain on our national character.

It will mean all asylum seekers arriving by boat can be processed at offshore facilities on Nauru and Papua New Guinea's Manus Island.

Previously, only people arriving on Ashmore Island, the Cartier Islands, Christmas Island and the Cocos Islands were subject to offshore processing.

The Howard government tried to excise the Australian mainland from the migration zone in 2006, but failed after a backbench revolt led by Liberal moderates.