UN refugee agency says it is 'deeply concerned' about transfer of Tamils, who fear torture or death at hands of Sri Lanka police

Australia has been accused of breaking international law and violating the refugee convention after returning a group of 41 Sri Lankan asylum seekers who attempted to reach the country by boat directly into the hands of the Sri Lankan navy.

The UN refugee agency, UNHCR, said in a statement that it was deeply concerned about the transfer, which took place on Sunday just off the coast of Sri Lanka. It comes amid a crackdown by the Australian government on asylum seekers who attempt to reach Australia by boat.

Sri Lankan officials confirmed on Monday that all 41 were handed over by the navy to the police and charged with illegally departing the country after their boat had been intercepted by a vessel used in the Australian military-led border regime Operation Sovereign Borders, near the remote Australian territory of the Cocos Islands. The handover, which took place last month, followed a week of speculation that two boats carrying about 200 Sri Lankan asylum seekers had been intercepted by Australia and turned back towards the Indian Ocean island.

Australia's immigration minister, Scott Morrison, has refused to divulge any details about the second boat – which departed from Pondicherry in southern India on 13 June and is understood to be carrying 153 Tamils, including 37 children – other than to say it was now outside Australian waters.

A number of those on board have contacted journalists and refugee advocates by satellite phone pleading for help.

An immigration source speaking to the Guardian said the second boat had been intercepted by Australian customs off the coast of Christmas Island last week and it was likely that it would also be handed over to the Sri Lankan navy.

Lawyers working for 48 of those on board were granted an interim injunction against any transfer to the Sri Lankan authorities after a dramatic last-minute high court appeal that resumes on Tuesday .

A Sri Lankan police spokesman, Ajith Rohana, said on Monday that the asylum seekers could face reprisals: "The sentence for those proved to have left illegally is two years of rigorous imprisonment and a fine. But if there are any facilitators, then they will be tried even if they have left via an authorised port legally."

Fifty-three legal scholars from 17 Australian universities warned that the government's attempts to rapidly screen the 41 asylum seekers' protection claims by teleconference while at sea did not "comply with the minimum standards on refugee determination under international law".

They added: "Holding asylum seekers in this manner also amounts to incommunicado detention without judicial scrutiny."

The stinging criticism follows "profound concern" articulated by the UN refugee body at the handling of the case and numerous calls for transparency from opposition politicians in Australia.

"UNHCR is deeply concerned by Australia's announcement that it has returned some 41 asylum seekers to Sri Lanka after having intercepted them at sea, as well as the fate of a further 153 asylum seekers of Sri Lankan origin who are now subject to an Australian high court injunction on their return," the UN body said in a statement.

"Without further information, UNHCR is not in a position, at this time, to confirm whether they were in accordance with international law. UNHCR has previously made known its concerns to Australia about its enhanced screening procedures and their noncompliance with international law."

It added: "UNHCR's experience over the years with shipboard processing has generally not been positive. Such an environment would rarely afford an appropriate venue for a fair procedure."

The Australian Greens' leader, Christine Milne, said that handing the asylum seekers to the Sri Lankan authorities in this manner was akin to "sending the persecuted back to the persecutors".

Morrison has described claims that Australia was violating international law as offensive and labelled criticism of his silence over the fate of the two boats "shrill and hysterical".

Morrison said: "The Australian government will continue to act in accordance with our international obligations, including applicable international conventions and to protect the safety of life at sea. At the same time we will not allow people-smugglers to try and exploit and manipulate Australia's support of these conventions as a tool to undermine Australia's strong border-protection regime that is stopping the boats and the deaths at sea."

Successive Australian governments have maintained close ties with the Rajapaksa regime in Sri Lanka. In November the new coalition government donated two Bay-class patrol boats to the Sri Lankan navy to help intercept boats carrying asylum seekers out of the country.

In contrast to the UK, Australia did not support a United Nations Human Rights Council motion to investigate alleged war crimes committed during the Sri Lankan civil war, which ended in 2009.

When asked about the fate of those on board the two boats, Australia's prime minister, Tony Abbott, said last week: "Sri Lanka is not everyone's idea of an ideal society, but it is at peace."

Since 2012, more than 1,000 Sri Lankan asylum seekers have been returned by the Australian government. An investigation by the Guardian and the Human Rights Law Centre revealed that Australian authorities in Colombo ignored claims that a returned asylum seeker had been tortured in Sri Lankan prison, sparking criticism that Australia employs a strategy of "wilful blindness" to the plight of those returned.

Earlier this year, Amnesty International described the treatment of dissidents by Sri Lankan authorities as deeply disturbing.

On Monday the Tamil Refugee Council of Australia published a statement from a relative of a three-year-old girl on board the second boat. "I am desperate to know where my family is. I can't function at all not knowing. I know all of them would be in very big trouble if sent back to Sri Lanka," the man said through an interpreter.

I want to plead with the Australian minister to stop our pain and let us know what he has done with all the kids and families on the boat. I ask him to be kind to these people. They are all very frightened. They cannot be sent back to Sri Lanka. Many of them will be tortured again and even killed."