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The Australian Immigration Minister Chris Bowen has brushed off reports Malaysia will not take asylum seekers who arrive in Australian waters before the two countries finalise a refugee swap deal.

Twelve days ago the Government announced Malaysia would take 800 asylum seekers in return for Australia resettling 4,000 Malaysian refugees.

Since then more than 100 asylum seekers have been intercepted in Australian waters.

The Australian Government says they will all be processed overseas, even though it has not finalised the deal.

But a Malaysian newspaper has quoted Malaysia's Home Affairs Minister, Datuk Seri Hishammuddin Hussein, as saying Malaysia will only accept asylum seekers who arrive in Australia after the agreement is finalised.

"On reports that a boatload of 32 asylum seekers temporarily housed at Christmas Island before being sent to countries such as Malaysia or Papua New Guinea where their refugee applications would be processed, Hishammuddin said the batch was not part of the transaction as the deal had not been finalised," the Malaysia Star reported.

Mr Bowen maintains Australia is still negotiating with Malaysia about what will happen to asylum seekers who arrive in Australia before the two countries finalise their refugee swap deal.

Mr Bowen says the Government is also negotiating with Papua New Guinea.

"What we've said about people who arrive in Australia from last Saturday, and this is the situation again consistently from now on, is that anybody who arrives in Australia will not be processed in Australia and has no guarantee of resettlement in Australia," he said on Tuesday.

"Of course, the prime ministers of Malaysia and Australia have agreed to the principles, senior officials have been working through some of the finer details. I expect that to be settled in coming weeks."

On Wednesday, a spokesman for Mr Bowen said the Government accepted that "no person will be sent to Malaysia until the arrangements are finalised".

On the weekend, Mr Bowen confirmed Australia would discuss with Thailand a deal similar to that agreed with Malaysia, and would also be interested in discussing such an agreement with Indonesia.

"We would have discussions with Thailand. I'm not pre-empting the results of that discussion," he said.

"We're not in formal discussions about a transfer agreement with Indonesia at the moment because my focus has been on Malaysia.

"But I do think this shows the potential for the sorts of agreements that could apply across the region."