Indonesia's foreign minister says the apparent addition of three extra passengers to an asylum seeker boat turned back into Indonesian waters is a "very serious development".

The asylum boat's crew reportedly told Indonesian navy investigators that two Australian warships put three extra people on board their boat - an Indonesian and two Albanians - before they were escorted back to Indonesian waters on Sunday.

Speaking at a leader's summit in Bali, foreign minister Marty Natalegawa said the information that people were put on the boat by Australian authorities was yet to be confirmed.

"I am informed that apart from the apparently original 18 asylum seekers who were in the original two boats, apparently some additional three individuals were added to the boat that was forced back to Indonesia," he said.

"So this is - if confirmed - obviously this is a very serious development.

"As I said from the beginning we are risking a slippery slope in the facilitation of Australia's Government for these individuals to be forced back to Indonesia."

Indonesia's navy has issued a statement based on testimony given by the crew, who were found on a wooden boat stranded on a small island in eastern Indonesia.

Boat timeline April 26: Captain Andre and three crew left South Sulawesi on board the KM Surya. Carrying 16 people from India and two from Nepal.

April 26: Captain Andre and three crew left South Sulawesi on board the KM Surya. Carrying 16 people from India and two from Nepal. April 30: Wooden boat reaches Semau Island and the captain got off the boat, took the GPS and documents and did not return. The crew continued their journey towards Ashmore Reef.

April 30: Wooden boat reaches Semau Island and the captain got off the boat, took the GPS and documents and did not return. The crew continued their journey towards Ashmore Reef. May 1 8:00am: The boat is in Australian waters. By midnight the boat was examined by two Australian warships.

May 1 8:00am: The boat is in Australian waters. By midnight the boat was examined by two Australian warships. May 2: The boat started being escorted back towards Indonesian waters.

May 2: The boat started being escorted back towards Indonesian waters. May 4 3:00am: An Indonesian and two Albanians were put onto the boat from Australian ships.

May 4 3:00am: An Indonesian and two Albanians were put onto the boat from Australian ships. May 4 5:30am: The KM Surya entered Indonesian waters.

May 4 5:30am: The KM Surya entered Indonesian waters. May 4 8:00am: The boat's engine died and it was stranded on Lay Island.

May 4 8:00am: The boat's engine died and it was stranded on Lay Island. May 4 10:00am: The boat and passengers were checked by Indonesian navy personnel.

May 4 10:00am: The boat and passengers were checked by Indonesian navy personnel. May 4 6:00pm: Handover letter for police was signed.

May 4 6:00pm: Handover letter for police was signed. May 5: Passengers handed over to local police. (Information released by Indonesian navy investigators, based on what they were told by crew)

The crew members say they were in Australian waters on May 1 while taking 18 asylum seekers from India and Nepal towards Ashmore Reef.

According to the crew, the Australian ships escorted them back to Indonesian territory a day later.

Indonesian navy spokesman Colonel Suradi Agung Slamet says the crew told investigators the extra passengers were put on the boat at 3:00am on Sunday and the boat re-entered Indonesian waters at 5:30am.

By 8:00am the boat's engine had died and it was stranded on Lay Island where it was checked by the Indonesian navy, crew members say.

In response to the claims, a spokeswoman for Immigration Minister Scott Morrison says the Government does not comment on "on-water operations".

Labor's immigration spokesman Richard Marles says the allegations are very serious.

"We need to hear from the Government immediately that what they are doing on the high seas is consistent with Australia's international obligations, with the covenants to which Australia is a party, and particularly the protocol against the smuggling of migrants by land, sea and air," he said.

Sorry, this video has expired Australian PM and Indonesian President agree to meet next month ( Indonesia correspondent Helen Brown )

"We need to be hearing from the Government right now. I understand that these allegations to date are not tested, but where allegations of this kind have been made in the past, we've heard from the Government almost immediately. We need to hear from them now, that what they are doing is consistent with our international obligations.

"My concern right now is that the silence is deafening."

Greens leader Christine Milne says she is shocked by the reports and if true, it would be in complete contravention of international law.

"These are really serious breaches of not only international law, but of appropriate process," she said.

Abbott calls SBY over cancelled trip to Bali summit

Meanwhile, Prime Minister Tony Abbott has called Indonesian president Susilo Bambang Yudhoyono, after cancelling his own trip to the Bali summit at short notice last week.

A spokesman for Mr Abbott says the pair spoke on the phone and committed to continue working on resolving current tensions in the relationship.

"In a very cordial conversation, both leaders agreed on the importance of the bilateral relationship between Australia and Indonesia," the spokesman said.

"They committed to continue the progress that has been made to resolve current issues and to strengthen the relationship further."

The Indonesian president's office said Mr Abbott used the call to express regret at not being able to travel to Bali.

The Bali trip was to have featured Mr Abbott's first meeting with his Indonesian counterpart since relations soured last year over spying revelations.

The ABC understands Mr Abbott pulled out because of an asylum seeker "operation" that Australian Government sources told the ABC had the potential to cause "embarrassment" to the Indonesian government.

The Government said the visit was cancelled to allow Mr Abbott to concentrate on next week's federal budget.