Customs and Border Protection cannot confirm that the boat which sank in Australia's search and rescue zone was intact and afloat when it was first seen by a commercial ship.
While 27 people - believed to be Sri Lankans - have been rescued, one person is dead and there are grave fears for 11 still missing after their boat sank 350 nautical miles off the Cocos Islands.
The Australian Maritime Safety Authority (AMSA) received a distress call from the boat early on Sunday morning.
AMSA called on ships in the area to go to its aid. Nine hours later a Taiwanese fishing boat arrived at the scene and reported that the boat was taking on water.
Several hours after that, a liquefied natural gas carrier also turned up and at that stage, it is believed the boat was still afloat.
Customs says it cannot confirm information obtained by the ABC that the boat sank when the LNG carrier was only several hundred metres away and in visual range.
Meanwhile, a Japanese fishing boat will join the full-scale air and sea search currently underway replacing the one from Taiwan which has left to refuel.
The fishing boat will join the LNG tanker now carrying the majority of the survivors, but no Australian boats are in the area.
A plane has been searching for survivors overnight and eight more are continuing the search.
Home Affairs Minister Brendan O'Connor says Australian authorities and the commercial boats are still searching for survivors.
"At this point the focus has been on rescuing those that were in the water, and for that reason we've now got up to seven aircraft and have now a Japanese vessel going to the assistance of the LNG Pioneer, to provide whatever help we can, to see whether we can rescue what could be up to 11 others," he said.
"There's been no confirmation in terms of the nationality of these passengers rescued from sea.
"The entire focus of the commercial vessels and the Australian aircraft has been to recover all passengers that were in the water after the vessel sunk late Sunday night."
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