The UN refugee agency says it is awaiting an explanation from the Australian Government over reports asylum seeker boats have been forcibly returned to Indonesia.

Earlier this week, Indonesian police told the ABC that a second boat carrying asylum seekers had been forced back to Indonesian waters by the Australian Navy.

The first boat was found shortly before Christmas on the island of Rote, in Indonesia's East Nusa Tenggara region.

The United Nations Refugee Agency (UNHCR) is warning such actions may place Australia in breach of its obligations under international law.

"UNHCR is seeking details from the Australian parties about these recent reports," said spokesman Babar Baloch.

But Minister for Immigration and Border Protection, Scott Morrison, has insisted that "border protection is a matter of national sovereignty".

"The Government is taking the steps necessary to protect our borders consistent with our domestic laws and international obligations," he said in a statement.

"The UNHCR has been a long term opponent and critic of the Coalition's strong border protection policies both in Government and in Opposition."

A spokeswoman for Mr Morrison confirmed a letter was sent to Operation Sovereign Borders last Friday.

The spokeswoman said Mr Morrison will review the letter when he returns to work from leave on Monday and the Government will provide a response next week.

The UN agency is also investigating reports of plans to provide lifeboats for asylum seekers for future push-backs.

"For the UNHCR it's a very concerning policy or practice if it involves pushing asylum seeker boats back out to sea without proper consideration of individuals who need international protection," said Mr Baloch.

"Any such approach would raise significant issues and potentially could place Australia in breach of its obligations under the Refugee Convention and international law.

"If people who are in need for international protection seek a country's safety, then they must be allowed to go through a process which helps to determine if these people are in need."

Last reported push backs about five years ago: UN

The UN refugee agency says its staff in Indonesia have been interviewing people who were onboard the two boats in question.

Mr Baloch said about 47 people were onboard the boat that was allegedly pushed back on December 19 and they were mostly African asylum seekers.

"The other group, on the 6th of January, [consisted] of around 45 people," he said.

The UNHCR says it is the first report of boats being turned back from Australia in five years and it wants to hear the Government's side of the story.

"We haven't heard in a long time [about] any push backs from the Australian territories," said Mr Baloch.

"We have not heard back, so far, from the Australian Government - so that's why we are saying we are seeking more details.

"So far what we are picking up is media reports."

In the statement Mr Morrison also reiterated the Government's support for the UNHCR's resettlement program.

"Despite our difference in views about what is necessary to stop the boats and the deaths at sea, the Government remains a strong supporter of the UNHCR international resettlement programme, most recently offering 500 of the 2000 places sought by the UNHCR for refugees from the Syrian conflict."

The UN is calling for increased regional cooperation and engagement in the Asia-Pacific to tackle people smuggling.