Federal Parliament has passed a motion condemning the Malaysian asylum swap deal, a move which opens the way for Greens legislation that could scrap the proposal.

The Greens motion, which had already passed through the Senate, is the first time a motion has passed through both houses condemning a Government policy and asking it to be withdrawn.

It passed through the House of Representatives 70-68 with the support of the Opposition, Greens MP Adam Bandt, who moved the motion, and independents Andrew Wilkie and Bob Katter.

Now Greens Senator Sarah Hanson-Young has introduced a bill amending the Migration Act to ensure Parliament would need to give its approval to any deal involving the expulsion of asylum seekers to a third country.

If the numbers in today's vote remain firm for the legislation, the Malaysian deal may be in jeopardy.

Senator Hanson-Young says she is confident the Opposition would support her bill despite differing with the Greens over many aspects of asylum seeker policy, including mandatory detention.

"It's not too late for the Government to walk away from this terrible deal," she said.

"But in the meantime, I believe any proposal where we are to export our international obligations, our compassion, our humanity, must come before the Parliament. It shouldn't simply be up to the government of the day."

While the Greens oppose the Malaysian solution on humanitarian grounds, the Opposition believes the Howard government's Pacific solution should be revived and the detention centre on Nauru reopened.

Immigration Minister Chris Bowen agreed that if the legislation was passed the Malaysian deal could not get through parliament.

"And neither would any other arrangement. If a future government tried to do something, with Nauru for example, that wouldn't get through the Parliament either," he told News 24.

But he said the Government does not need to legislate for the Malaysian deal because it is using legitimate powers under the migration act.

"Of course, we would not be supporting the Greens amendments and I would be astounded and disappointed if the Liberal Party did because it would be extraordinarily hypocritical," he said.

Opposition Leader Tony Abbott says if the Malaysian deal goes ahead it will be "in clear defiance" of Parliament.

"We are in uncharted waters here," Mr Abbott told reporters.

"[But] If the Greens want to be taken seriously it's not enough to move non-binding resolutions in the Parliament, they're going to have to force some changes on their alliance partner in Government."

Opposition Immigration spokesman Scott Morrison says the Malaysian deal should now be dropped.

"This is a significant outcome, it hasn't happened at least in the memory of most in this place and I think that's a savage indictment of the government's handling of this matter," he said.

Senator Hanson-Young says her bill would allow parliament to scrutinise the Malaysian deal and ultimately decide if it, or any other third-country deal, should be approved.

"As there have been many fears raised by MPs and senators about the impending expulsion of unaccompanied children and families to Malaysia and elsewhere, it is fitting that they be given their say in the parliament," Senator Hanson-Young said.

"Parliament needs to have its say, because these third country deals carry heavy costs to taxpayers, as well as Australia's reputation for compassion and humanity."

Talks with UN

Immigration Minister Chris Bowen has confirmed a government delegation is in Geneva to negotiate with the United Nations High Commissioner for Refugees over the Malaysia refugee swap deal.

But he denied negotiations have been tougher than expected with the UNHCR, which needs to approve the deal if it is to go ahead.

"The UNHCR is based in Geneva so it's pretty unsurprising there would be a meeting in Geneva to talk about the finer operational details of this arrangement," Mr Bowen said.

And he confirmed a delegation from Malaysia is involved in the Geneva talks.

"The negotiations have been held in the spirit of very good will between Australia, Malaysia and the UNHCR. It's a bilateral agreement between Australia and Malaysia but we've been consulting closely with the UNHCR."

Mr Bowen says the talks involve the tricky question of how to look after unaccompanied children on boats without simply allowing them to stay in Australia.

He says that would just give people smugglers the incentive to stack boats with children.

"When you have children arrive you need very sensitive arrangements in place to ensure that any particular vulnerabilities are dealt with and taken into account.

"That is the case in the arrangements we've been discussing with Malaysia and the UNHCR."

"Nobody wants to see children getting on boats. That's our motivation. I don't want to see Australia go through what we went through last December of having to bury children."

"That's a terrible thing, a terrible thing for everybody involved and everything should be done to avoid that."

The UNHCR also wants to ensure guarantees are in place to safeguard the human rights of asylum seekers sent to Malaysia which has laws that allow caning for breaches of discipline.

Under the deal, Australia will accept 4,000 refugees currently in Malaysian detention centres in return for Malaysia accepting 800 people seeking asylum in Australia.