At least 13 people have died and dozens are missing after a boat carrying suspected asylum seekers sank near Australia, officials say.

Australian Home Affairs Minister Jason Clare said on Sunday that aerial surveillance spotted 13 bodies among a debris field of wood and life jackets near the remote Chrismtas Island. He added that a full-scale hunt involving 15 ships and 10 aircraft was under way to search for survivors.

"This is a search and rescue, trying to find people alive," Clare told reporters, describing the incident as "another terrible tragedy, another terrible reminder how dangerous these journeys are".

Clare said officials counted about 55 people on the deck when the drifting boat was first spotted by a border protection aircraft on Wednesday. They were mostly adult men but also a small number of women and children.

The navy vessel HMAS Warramunga was sent to intercept the boat on Thursday but it had disappeared, and aerial searches turned up no sign until Friday, when Clare said a "submerged hull" was seen from the air.

The Warramunga arrived on site to find wood and life jackets floating, with the first body sighted late on Friday and another 12 found by Sunday morning.

Rear Admiral David Johnston, the head of border protection, said the "complex and time-consuming" task of recovering bodies would not begin until the search for survivors was over.

Hundreds of refugees have died in boat accidents on the perilous sea journey from Indonesia to Australia in recent years.

Australia is struggling with a record influx of refugees arriving by boat from Indonesia and Sri Lanka, with numbers expected to top 25,000 in the 12 months since last June.