Draft laws stopping foreign fighters from returning to Australia for up to two years are likely to pass parliament after Labor failed in its bid to amend the bill.
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Labor initially tried to push the legislation back to parliament's intelligence and security committee for further scrutiny.
Shadow attorney-general Mark Dreyfus' 40 amendments, centred on recommendations from the bipartisan committee, were also voted down.
The opposition had wanted 18 recommendations from the committee adopted - including two changes the government has rejected - but supported the bill anyway on Tuesday night.
Five of the lower house's six crossbenchers - Greens MP Adam Bandt, Andrew Wilkie, Zali Steggall, Helen Haines and Centre Alliance's Rebekha Sharkie - cut lonely figures as the only MPs opposing the bill.
The proposal is now on its way to the Senate, where Centre Alliance will attempt to amend it.
Ms Sharkie said it was essential the legislation included all the committee's recommendations, urging the government to also release legal advice on its constitutional certainty.
During debate over the bill she asked Labor to reconsider its support, describing it as "alarming" the opposition were "willing to wave it through".
Labor is concerned the legislation is not descriptive enough about the powers it grants the home affairs minister, and worried the laws might not be constitutionally sound.
Home Affairs Minister Peter Dutton said the two recommendations rejected by the government would undermine and weaken the scheme, as the threshold for netting people would be too high.
Labor's home affairs spokeswoman Kristina Keneally wrote to Mr Dutton earlier this week asking for the committee to reconsider the legislation and to release legal advice on its constitutionality.
The proposal builds on laws introduced to parliament in February, before the legislative slate was wiped clean at the election.
Under the proposal, any citizen suspected of extremism would be temporarily banned from returning to Australia until protections are in place through a so-called "return permit".
The bill establishes a reviewing authority to provide independent oversight of the minister's decision to create a temporary exclusion order.
Return permits may include conditions relating to when and how the person enters the country, and they may also have to register where they live, work or study and any plans to travel within Australia or abroad.
The proposed 12-month return permit could also include conditions around using technology.
Mr Dreyfus accused the coalition of using "cheap smears" to try and wedge Labor on the legislation.
He said the opposition was not "turning its back" on national security by wanting greater oversight and scrutiny of the legislation.
"There is a very long and a very sorry history of accusations of history or disloyalty being thrown about for base political purposes," he told parliament.
"By going down that path, this government is aping a political technique that is being used by some of the worst regimes in history."
Liberal MP Andrew Hastie, who chairs the parliamentary committee, said he was satisfied with the government's proposal.
He said the exclusion orders were needed as fighters were returning to Australia with "combat experience, hard hearts and a proven capacity for violence and bloodshed".
Australian Associated Press