The United Nations high commissioner for Human Rights has questioned Australia's asylum seeker deal with Malaysia, saying the plan could violate international law.

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

UN high commissioner Navi Pillay used her speech at a forum in Sydney last night to remind the Australian Government about its human rights obligations to asylum seekers.

She told the forum of her concerns about the deal with Malaysia, a country that has not ratified conventions on torture or refugees.

Ms Pillay appealed for Australians to be more humane to asylum seekers, who she said were still entitled to human rights.

She says the deal may violate international law.

"If Australia is serious about this policy of sending 800 people out to Malaysia, then I think it violates refugee law," she said.

"They cannot send individuals to a country that has not ratified the torture convention, the convention on refugees.

"So there are no protections for individuals in Malaysia. And if Australia, of all people, that upholds [international standards], should not collaborate with these kinds of schemes."

Ms Pillay also spoke of her distress over Australia's mandatory detention policy, something she said was not effective and cost Australia too much money.

She says the Malaysia deal will be expensive and Australia would be better off concentrating on speeding up the time it takes to process asylum seekers.

Ms Pillay says there is no date on when people can expect to enter Australia having gone through a process.

"The process should be legal and it should be expedited," she said.

"Resources should be spent on speeding up the process rather than investing these huge amounts of money on detention centres and shipping people out to Malaysia and having them join a queue and offering them the possibility of 'I don't know when it will happen'."

Refugee advocates have welcomed Ms Pillay's comments.

Obligation

Human Rights Law Centre executive director Phil Lynch says the Government should abandon the deal with Malaysia.

"I would say that Australia's obligation is to provide protection to those people who lawfully seek asylum under the Refugees Convention," he said.

"That is Australia's international obligation, it is our moral obligation, it is our human obligation."

Ms Pillay is likely to raise her concerns when she meets Prime Minister Julia Gillard in Canberra today.

The Government says it is certain its plan to process refugees in Malaysia is lawful, but nonetheless is expecting legal challenges.

It was left to Immigration Department secretary Andrew Metcalfe to explain the strategy during Senate estimates last night.

"The Australian Government is quite confident, very confident of the lawfulness of this policy and this approach," he told the hearing.

"We've seen that this is a contested area of public policy, not only at the political level but... between the Government and various advocacy groups."