Forty-one asylum seekers returned to Sri Lanka by Australian authorities are being handed over to criminal investigators in the port city of Galle.

Sri Lanka's navy has confirmed it received the asylum seekers from Australia on Sunday morning in a mid-sea transfer in waters south of the island nation.

Immigration Minister Scott Morrison gave details on the case for the first time today, after more than a week of silence on the fate of two boats which were believed to have been intercepted north-west of Australia late last month.

He said the asylum seekers' boat, intercepted west of the Cocos Islands, was carrying 37 Sinhalese and four Tamils from Sri Lanka.

In a statement, Mr Morrison said the 41 people on board were scanned by teleconference at sea before being transferred to the Sri Lankan navy.

But he refused to discuss the whereabouts of another 153 asylum seekers on another boat believed to be facing the same fate.

Officials say the asylum seekers, all men, will be taken to the port of Galle today and handed over to the Criminal Investigation Division, which is an arm of the intelligence branch.

It is a crime to leave Sri Lanka without leaving by an official port, so people who are caught at sea and returned are often charged with illegal migration offences.

"They will be charged under the Immigrants and Emigrants Act," police spokesman Ajith Rohana told the Reuters news agency.

"The sentence for those who are proved to have left illegally is two years of rigorous imprisonment and a fine."

Sri Lankan authorities will also be trying to establish if any of the men have any links to any militant groups, which officials say is why the intelligence department must screen them.

A Sri Laankan navy spokesman said it is usually a very quick process, and that the men should appear before a magistrate within 24 to 48 hours.

He said there had been 4,300 people processed and "99.999 per cent" had been released almost immediately.

But human rights lawyers dispute that, and say detainees are held under terrorism laws for up to 28 days or longer. What happens to them is unclear, but human rights lawyers say they face torture and other cruel measures while being held.

The navy spokesman said he did not have any information about plans to transfer more asylum seekers in coming days or weeks.

One asylum seeker 'opted to return', others given no choice

The Government says one of the Sinhalese may have had a case for seeking asylum, but opted to be handed back to Sri Lanka after being told they would be sent to Manus Island or Nauru for offshore processing.

The statement also said that all of the people on board were "safe and accounted for" and the boat was not in distress.

"This is how you stop the boats. This is how it has to be done because this is what works," Mr Morrison said.

Greens immigration spokeswoman Sarah Hanson-Young has criticised the screening process, which reportedly involved just four questions via teleconference.

"A telephone conference of four questions - really, if it wasn't so serious, if it wasn't about life and death, it'd be laughable," Senator Hanson-Young said.

Shadow minister for immigration Richard Marles has also questioned the operation.

"Australia's international obligations are reliant upon a credible processing system and we have deep concerns about how that could have been performed by video link at sea in a way which gave an individual assessment, when all the time the boat was steaming towards Sri Lanka," Mr Marles said.

The Refugee Action Coalition's Ian Rintoul says the Government's screening processes are not adequate.

"You've handed people who are fleeing persecution in Sri Lanka back to the Sri Lankan government," Mr Rintoul said.

"It's a complete violation of their human rights and the refugee convention.

"Those people should have been brought to Australia and had their claims properly assessed and settled in Australia if they were found to be refugees."

Legal scholars say transfer may have violated international law

Fifty-three legal scholars from 17 Australian universities say they are "profoundly concerned" the asylum seekers were subjected to "rapid and inadequate screening interviews at sea" before being returned to Sri Lanka.

In a statement, the academics say the Government's actions in returning the asylum seekers to their country of origin "raises a real risk of refoulement."

Sorry, this video has expired International law expert Don Rothwell speaks to the ABC

Refoulement is an international law term that refers to the involuntarily return of refugees to their country of origin in cases where they may face severe human rights abuse or persecution.

The scholars said returning the asylum seekers would breach Australia's obligations under international refugee and human rights law, including the 1951 Refugees Convention, 1948 Universal Declaration on Human Rights, and the 1966 International Covenant on Civil and Political Rights.

They also questioned the legality of holding the asylum seekers at sea.

"Holding asylum seekers on boats in this manner also amounts to incommunicado detention without judicial scrutiny," they said in a statement.

"We urgently call on the Australian Government to make public its legal justification for this operation."

Sri Lanka has not directly commented on whether Australia has acted lawfully.

Uncertainty remains over boat intercepted off Christmas Island

It is still not known what happened to the other boat, which was said to be carrying 153 people and was intercepted off Christmas Island more than a week ago.

Senator Hanson-Young says the Government needs to reveal the fate of those on that boat.

"The majority of them, my understanding is, are Tamil asylum seekers, including 37 children. Now, they are still being held in custody on board a customs vessel," she said.

"They haven't been handed over to the [Sri Lankan] Navy as yet and the Government needs to start being up front with what's happening to them and what their fate will be."

The Tamil Refugee Council claims at least 11 people on that boat have been tortured by Sri Lanka's intelligence services, adding there must have been more people on the ship in a similar situation.

The Tamil asylum seekers reportedly fled Sri Lanka to a refugee camp in India before boarding a boat to Australia.

Mr Morrison, Foreign Minister Julie Bishop and other senior government ministers have all deflected questioning about the boats, repeating that the Government does not comment on operational matters.

Senior Coalition Minister Eric Abetz yesterday denied the Government was "disappearing" asylum seekers, insisting that Australia would continue to uphold its international obligations in relation to those matters.

Mr Morrison will visit Sri Lanka this week to attend a commissioning ceremony for two former Australian Customs patrol vessels gifted to the Sri Lankan government.

The Opposition raised concerns at the time of the decision to pass on the patrol boats, saying there should be clear guidelines placed on their use.

The Greens said that the boats would be used to stop Tamils fleeing persecution and human rights abuses.