The crew of an asylum seeker boat turned back to Indonesia by the Australian Navy says three extra passengers were added to their boat from the Australian ships.

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.

The three crew members reportedly told navy investigators two Australian warships put three extra people on board their boat - an Indonesian and two people from Albania - before they were escorted back to Indonesian waters on Sunday.

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 3am on Sunday and the boat re-entered Indonesian waters at 5:30am.

By 8am 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".

Greens leader Christine Milne says she is shocked by the reports.

She says if they are 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.

"My question is: is this something Scott Morrison directed his department to do, is this something Tony Abbott knew about?"

Last week, Prime Minister Tony Abbott cancelled a planned trip to Bali due to an "on-water operation", which Australian government sources believe 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.