Immigration Minister Chris Bowen says unaccompanied children will be among the asylum seekers sent from Australia to Malaysia as part of a refugee swap.

In May, the Federal Government agreed on an in-principle refugee swap that would see Australia resettle 4,000 Malaysian-based refugees in return for Malaysia accepting 800 asylum seekers.

The final deal between the two countries has not been signed, but the ABC's Lateline program has obtained a draft document which shows Malaysia has removed references to human rights.

It also confirms that Malaysia wants a veto over the 800 people that Australia sends there, and also wants Australia to cover nearly all the costs.

Mr Bowen says the deal should only be judged when it is finalised, but he says he will not put in a clause to exempt unaccompanied children.

"You need to send a strong message," he said.

"I don't want unaccompanied minors, I don't want children getting on boats to come to Australia, thinking or knowing that there is some sort of exemption in place.

"I never want to go through, and I don't want our nation to go through, what we went through in December and the months following, burying children as a result of a boat accident.

"And it is inevitable that that will occur again unless we break the people smugglers' business model."

Mr Bowen also points out that the Lateline documents are a draft and the final deal has not been reached.

"The Malaysian government has been very clear [in its] commitment to deal with those people in a way which respects their dignity, which respects human rights standards, and that is why organisations like the UNHCR have been involved in these discussions," he said.

Greens Senator Sarah Hanson-Young says Mr Bowen has a special responsibility for unaccompanied asylum-seeker children.

"The minister forgets that he is legally the guardian of unaccompanied minors," she said.

"The minister, for the sake of a political quick-fix, is prepared to expend the rights and obligations he should be offering to these very, very vulnerable children."

Senator Hanson-Young also insists that specific protections for human rights must be included in the final deal between Australia and Malaysia.

"The Prime Minister specifically said that human rights must be respected," she said.

"Human rights has been deleted from the document in negotiation with Malaysia; human rights is not clearly the bottom line for either Malaysia or, you would have to argue, Australia."

The document states the asylum seekers will be subject to Malaysian laws. It also says those issued with a UN refugee agency card will be treated with "dignity and respect".

Mr Bowen says Malaysia has given assurances that the asylum seekers sent there will have their human rights respected, but refugee lawyer David Manne says the documents reveal Malaysia's reluctance to commit to human rights standards.

"There is no reference to the word asylum seeker. There is certainly no reference to human rights," he said.

Opposition immigration spokesman Scott Morrison says the wording of the document is not enough to guarantee asylum seekers human rights.

"I don't think that is enough, because Malaysia has not signed the refugee convention, it has not signed the convention against torture and degrading treatment," he said.

"It does not have the same record of international engagement on these issues as Australia, and clearly it needs more than a couple of words to breach that gap - and we have these undertakings from Nauru."

UN approval

Richard Towle, the regional representative of the United Nations High Commissioner for Refugees (UNHCR), which is working on the refugee swap deal, says the agreement must include specific human rights protections.

"It's incumbent on both parties to the agreement to make sure those children and women and vulnerable torture victims are taken care of appropriately," he told Lateline.

"And it's very important to have a monitoring and an oversight mechanism to ensure they [receive] the kind of protection they need."

But Mr Towle says the deal is still under discussion.

"We hope that the agreement will be judged on its final terms, not according to one piece of a part of a negotiation that has been going on for some months," he said.

"It's no secret we have had some difficulties with part of the process.

"That is why we have come back and said in our view we want to see some good clear protection standards for the people returned."