Greens leader Christine Milne has slammed Labor for backing a plan they were strongly opposed to in 2006.
Federal Labor, with the backing of the coalition, today successfully steered its controversial excision legislation through the Senate.
It paves the way for people arriving by boat to be processed at offshore facilities on Nauru and Papua New Guinea's Manus Island.
"The nation was horrified that a prime minister would seek to wipe Australia off the map," she said, recalling John Howard's failed attempt to excise the Australian mainland in 2006.
"This legislation that we are debating here today is a stain on our national character."
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Under the Migration Amendment (Unauthorised Maritime Arrivals and Other Measures) Bill 2012, mainland Australia will join Ashmore Island, Cartier Islands, Christmas Island and Cocos Islands out of the migration zone.
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.
Manager of government business in the Senate Jacinta Collins earlier on Thursday succeeded in fast-tracking the bill through the upper house.
She said people smugglers were evolving their tactics. In early April 66 Sri Lankan asylum seekers sailed into the Western Australian port of Geraldton after travelling more than 5000km, stunning onlookers.
Liberal senator Michaelia Cash said the coalition strongly supported the bill.
She claimed Immigration Minister Brendan O'Connor came to coalition MPs "quite literally on bended knee" on Thursday and "begged" them to support the government's legislation.
A spokeswoman for Mr O'Connor denied the minister held any meetings with the coalition about the legislation on Thursday.
Greens senator Sarah Hanson-Young said Labor was "doing all the Liberal Party's dirty work" in "beating up on refugees, dog whistling on immigration and stripping away laws that protect the most vulnerable in our community".
Australia was contravening the United Nation's refugee convention by discriminating against asylum seekers based on their mode of arrival, she said.
The government was creating a "damaged generation" by keeping children in detention.
"We are subjecting these children to child abuse, to institutionalised abuse," Senator Hanson-Young told parliament.
The amended government bill now goes to the lower house for a final tick of approval.
An earlier version of the bill passed the House of Representatives in November.
