Australian authorities have turned back a boat of Sri Lankan asylum seekers after intercepting them near the Indonesian coast, Immigration Minister Scott Morrison said.

Mr Morrison said the asylum seekers, who were first spotted two weeks ago, were handed over to Sri Lanka's navy and arrested on Thursday.

He confirmed that while 37 of the asylum seekers were transferred, one remains in the care of Australian authorities and will go through the process of being considered a refugee.

"There is one individual who is being transferred to offshore processing facilities to further look into information that he provided regarding his own situation but all 37 of the other passengers were returned," he said.

"There is no greater deterrent to protecting our borders and stopping boats coming to Australia than by stopping the boats physically and returning those vessels from whence they came."

Mr Morrison said he was confident those being returned would be safe in Sri Lanka.

"I'm very confident we've acquitted our obligations under the convention and various treaties as this Government has and as previous governments have," he said.

Sri Lanka's superintendent Ajith Rohana said investigations were ongoing.

"The boat left Sri Lanka on November 1," Mr Rohana said, adding that six children were among the passengers.

"Investigations are being conducted by the anti-people smuggling unit of the CID (Criminal Investigation Department).

"They are being held in custody but will be taken before a magistrate shortly."

Palaniappan Kumarasamy from the Australian Tamil Congress said there were fears the returning asylum seekers would be persecuted if they were linked to the separatist Tamil Tigers.

"If the Sri Lankan Government think that these people are involved in the past with the LTTE then of course their life will be in danger," Mr Kumarasamy said.

"They may be imprisoned and tortured.

"We do not know what is happening to these people once they are taken to the Sri Lankan army camp."

Opposition leader Bill Shorten said the latest turn back raised concerns about the Government's openness with the public.

"Yet again we see the Federal Government's immigration boat turn back policies shrouded in secrecy," Mr Shorten said.

"The whole story of the last year and a quarter of the Abbott Government is that they just don't trust Australians or bring them into their confidence."

Minister defends asylum policies from UN criticism

The Immigration Minister brushed off criticism of Australia's hardline asylum seeker policies after stinging criticism from the United Nations Committee Against Torture.

The Geneva-based organisation has released a report expressing concerns on several policies including Australia's use of offshore processing and mandatory detention.

It has raised concerns about the impact these policies have on asylum seekers, and recommends using detention as a last resort and giving people access to legal assistance.

But Mr Morrision insists Australia is meeting its international obligations.

"Well we'll look at these matters as they're invariably raised but what I want to assure Australians is [that] Australia's border protection policies are made in Australia, nowhere else," he said.

Morrison announces new Myanmar border deal

The Sri Lankan asylum seekers turned back were the first since July, when a boat loaded with 41 nationals was intercepted by Australia.

Sri Lanka charged them with illegally leaving the country, and their cases are due to be taken up by a court next May.

Australia has gifted two vessels to Sri Lanka's navy to patrol its shores and stop boats leaving the island, as part of Canberra's border protection policy.

Australia faces international censure over its treatment of asylum seekers who are denied resettlement in Australia and sent to camps in Papua New Guinea and Nauru.

Meanwhile, Mr Morrison announced Australia would help review Myanmar's border management plans under a new deal.

The Immigration Minister said the review was part of a five-year Memorandum of Understanding that has been agreed to by the two nations.

The plan would be developed with the assistance of Australia's Immigration Department.

Mr Morrison said that when the region has stronger borders, then Australia has stronger borders.

ABC/AFP