The Immigration Department says Australia has paid for the "not insignificant" legal costs of the Papua New Guinea and Nauru governments in fighting to keep asylum seeker detention centres open.

It means Australia is paying for the PNG government's defence in a constitutional challenge by PNG opposition leader Belden Namah.

In Senate Estimates today, Immigration Department secretary Martin Bowles confirmed the general amount being spent on offshore detention legal cases.

"It is in the order of around $350,000 to $370,000 in Manus," he said.

"We might have spent a little in Nauru."

The funding for PNG and Nauru’s legal costs comes from the Immigration Department's offshore processing budget.

Mr Bowles says paying Nauru and PNG's legal costs is in line with the Memorandum of Understanding (MOU) between the nations to run the centres.

"The original MOUs signed with both Manus and Nauru indicated the Australian Government would pay for the costs of activities in relation to transferees to both Manus and Nauru and legal costs is part of that cost, if you like, of what is happening," he said.

"So yes, the Australian Government has paid for that and has been doing so in various forms since the arrangements started in late 2012."

Mr Bowles confirmed under questioning by Greens Senator Sarah Hanson-Young that Australia paid for the PNG government's defence in a constitutional challenge by Mr Namah.

"We would have made payments to the PNG government or a party in relation to that and others I would imagine," he said.

"I can't recall the exact amounts of how we paid now, but it would not be insignificant."

Mr Namah's constitutional challenge is being considered by the PNG Supreme Court.

If successful, the case may undo the legal basis for the Manus Island processing centre.

'Unacceptable' use of taxpayer money: Greens

Refugee advocates say Australian money is also likely to have been used to quash Justice David Canning's inquiry into human rights' violations arising from February's violence at the centre.

Senator Hanson-Young says Australian taxpayers' money should not be used in this way.

"It's unacceptable that the Abbott Government is slashing support for pensioners, childcare and healthcare in Australia while paying other countries' legal bills," she said.

"The relationship with PNG and Nauru is a jurisdictional mess."

The PNG National Court started the inquiry, but it has been on hold since the PNG government launched a legal challenge.

Mr Bowles says Australia would most likely be funding that challenge.

"It relates to Manus Island, and again, under the MOU, it would not be unusual that we would assist with the funding for that," he said.

Daniel Webb from the Human Rights Law Centre wants more information.

"At the time, Scott Morrison was at pains to distance Australia's involvement with the appeal to halt the human rights inquiry, yet now it would seem that Australia may have been bankrolling it."

"The fact our Government pays another country's legal bills while at the same time refusing to fund legal assistance for asylum seekers here in Australia shows just how determined this Government is to deny asylum seekers a fair go."