The Greens say the Stronger Futures legislation debate was brought on in short notice so that the bills could be passed before a six-week parliamentary recess.
Greens Christine Milne expressed concerns over the effect it will have on Aboriginal people.
"What we are now going to see is greater disempowerment of Aboriginal people and their own efforts at self-determination undermined," she said.
Despite criticism from human rights groups and indigenous advocates, the federal government says the legislation is a big win.
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“This is very important legislation aimed at making sure that we have strong alcohol controls in Aboriginal communities,” said Indigenous Affairs Minister Jenny Macklin.
The senate passed the legislation after a debate that stretched into the early hours of Friday morning. The bills extend the Northern Territory intervention, introduced by the Howard Government in 2007, for another decade.
It allows for welfare quarantining and alcohol management, and cuts welfare payments for parents whose kids miss school.
“We want to work closely with the Northern Territory government to make sure that children go to school every day,” Ms Macklin said.
But the government is being criticised for not consulting enough with Indigenous people.
“The senate committee has found that those consultations were grossly inadequate,” said Jacqueline Philips from Australians for Native Title and Reconciliation, “and that there are high levels of distress, of anxiety, of confusion and opposition to these bills in communities.”
The human rights commission believes the legislation brings shame to Australia's rights record.
“Even though the law is not discriminatory,” said Social Justice Commissioner Mick Gooda, “the way it's implemented can have a disproportionate affect on Aboriginal people.”
The Human Rights Commission says it will keep a close watch on the way Stronger Futures is enforced to ensure it doesn't breach standards.
Despite The Greens' attempts to amend the bill, both major parties supported the legislation, consequently passing it through the Houses of Parliament.
Aboriginal elders have declared a day of mourning to mark the passing of the legislation.
