Merchant vessel Maersk Diadema was responding to a mayday call from AMSA on Monday when it steamed towards the asylum boat about 70 nautical miles southwest of Bali. AMSA, in turn, was responding to distress calls from someone onboard the asylum boat.
The crew of the MV Diadema, a 290m-long container ship, had finished bringing rescued passengers aboard from the small asylum boat when the Indonesian crew surprised them by getting back on to the wooden vessel, and headed for Indonesia.
"Six people returned to the rescued vessel and sailed away from the scene towards Indonesia," a spokesman from Customs and Border Protection Command told The Australian last night. "It's likely, based on their actions, that they were crew."
The incident has angered some inside Border Protection Command because the search for the boat diverted many resources, including an RAAF maritime surveillance aircraft.
The 62 asylum-seekers who stayed onboard the MV Diadema were met by Australian Customs Vessel Triton, which took them onboard and delivered them to Christmas Island.
The container ship resumed its path to Fremantle.
The incident occurred as the MV Parsifal responded to a separate mayday call to rescue adult men off Java; once onboard, the men threatened self-harm if the master continued to Singapore as planned and did not take them to Christmas Island.
The rescue effort for the boat the crew eventually sailed off in began at about 5.30am on Monday, according to AMSA, which said it received a call for assistance from a mobile phone being used by someone onboard.
The line was bad, an AMSA spokesman said, and with help from an interpreter it took until 5pm to determine the vessel's location, which was about 48 nautical miles south of East Java and inside the Indonesian search-and-rescue region.
Throughout the day, several locations were provided, which were each investigated by merchant vessels in the area. The location of the vessel was confirmed when it was sighted by a RAAF maritime surveillance aircraft under the co-ordination of AMSA.
The incident occurred as the group of 67 asylum-seekers rescued from their boat by the merchant ship Parsifal became agitated, threatened to harm themselves and demanded to be taken to Australia in a high-seas incident that has been compared with the 2001 Tampa crisis.
The Australian Federal Police last night confirmed it had interviewed the MV Parsifal's Singapore-based captain and a number of asylum-seekers over allegations they made threats after being pulled from a rickety boat, thought to have been taking water.
An AFP spokeswoman said the captain had indicated he did not wish to pursue the matter, but police were continuing to investigate.
The conflict erupted on Tuesday morning 30 minutes after the Parsifal's captain finished rescuing 67 male asylum-seekers from their boat, which was 50 nautical miles south of Sunda Strait, in the Indonesian search-and-rescue zone, and continued steaming towards Singapore.