The High Court has granted an interim injunction to block the handover of 153 asylum seekers to Sri Lanka, just hours after the Government confirmed another vessel had been returned.

On Monday the court heard an urgent claim from barristers seeking to protect the group, which includes 32 women and 37 children and is believed to be under the Government's control at sea.

"We argued that the asylum seekers are entitled to have their allegations - claims against the Sri Lankan government - heard and processed in accordance with the law," solicitor George Newhouse said.

"The Minister can't simply intercept them in the night and disappear them."

Mr Newhouse said he was shocked by revelations a separate group of 41 asylum seekers would face criminal charges in Sri Lanka after being returned.

"That strengthens the urgency of this court application because if this Government is putting those people at risk of criminal charges, imprisonment and torture - because that's what happens in Sri Lankan prisons - then these people need assistance urgently," he said.

He says the asylum seekers "claim they are fleeing persecution and that they are at risk of death, torture or significant harm".

Mr Newhouse says 48 of the 153 asylum seekers on the boat, including women and children, were named in court.

"The others we've sought protection for even though we were unaware of their names," he said.

Justice Susan Crennan declared it was probable the asylum seekers had been detained or were in the custody of the Navy and would be handed over to Sri Lankan authorities.

She ordered an interim injunction against any transfer until this afternoon, when the matter is set to be heard in the High Court.

A spokesperson for Immigration Minister Scott Morrison says the "Government notes the matter is currently before the court and accordingly will be making no further comment".

It is understood some of the asylum seekers fled Sri Lanka to refugee camps in India before boarding a boat to Australia.

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

The boat was intercepted off Christmas Island more than a week ago but Mr Morrison refused to comment on its fate.

Returned asylum seekers face 'rigorous imprisonment'

Earlier on Monday, Mr Morrison confirmed 41 asylum seekers had been handed over to Sri Lanka's military.

Mr Morrison said the group of asylum seekers already returned to Sri Lanka were intercepted on a boat west of the Cocos Islands.

The 37 Sinhalese and four Tamils from Sri Lanka were scanned by teleconference at sea before being transferred to the Sri Lankan navy on Sunday.

The Government said one of the Sinhalese might 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 asylum seekers were taken to the port of Galle and handed over to the Criminal Investigation Division, which is an arm of the intelligence branch.

Sri Lankan police say the group includes 28 men, four women, seven boys and two girls.

Space to play or pause, M to mute, left and right arrows to seek, up and down arrows for volume. Watch Duration: 7 minutes 46 seconds 7 m David Manne talks to 7.30

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 said.

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

He said investigators were yet to identify who among the asylum seekers organised the boat journey, but they faced a jail term of five years and were unlikely to get bail. He said none of the children would face charges.

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

Leading refugee lawyer David Manne says it is hard to predict what will happen to them next.

"This is part of the problem that we've seen in Sri Lanka with people being essentially summarily expelled there without proper due process," he told the ABC's 7.30.

"It's a country where there is an extremely serious systematic abuse of human rights ongoing in the country against a certain minority particularly, and it is often very difficult to precisely track the fate of a returned asylum seeker.

"There are profound concerns that [returning the asylum seekers] is not legal, that it is violating people's fundamental rights and putting people's lives at risk."

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 Refugee 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."

Greens senator Sarah Hanson-Young has criticised the Government's 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.

Opposition immigration spokesman 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.

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