Rescue efforts are continuing throughout a second night, but the operation has passed the critical 36-hour mark during which those lost have the best chance of surviving.
One hundred and nine asylum seekers were rescued on Thursday night, with one of the survivors being a 13-year-old boy.
So far there have been three confirmed deaths but that number is set to rise significantly, with rescuers now being ordered to retrieve bodies from the water.
The Australian Maritime Safety Authority (AMSA) says the aviation search will be scaled down throughout the night, but will return to full scale in the morning as naval and merchant vessels continue to scour the ocean for survivors.
AMSA says a full-scale search will run through until Saturday afternoon, when the operation will be reassessed.
108 adult men and one 13-year-old boy rescued so far
Critical 36-hour time period for survival has lapsed; rescuers ordered to start retrieving bodies
A Navy ship took 96 survivors to Christmas Island; three were taken to hospital
Three people confirmed dead and about 90 more remain missing
Four ships and several aircraft are on the scene searching for more survivors
Australian authorities say they knew the boat was in trouble early on Wednesday and told it to return to Indonesia
Look back at how events unfolded throughout Friday.
10:45pm Home Affairs Minister Jason Clare tells Lateline the rescue operation has passed the critical 36-hour mark and rescuers have been advised to find and retrieve bodies:
We've been searching all day; we've had planes in the air. We've had merchant vessels looking as well. All we've found is debris. We've found life jackets floating out there, but we haven't found people alive. We've seen a lot of dead bodies.
Boarder Protection Command have now instructed the men and women that are out there in the search-and-rescue area to now identify people that have perished and retrieve their bodies.
We're now passed that key 36-hour zone when I am told we've got the best chance of saving people's lives. The water is warm – it's 29 degrees – but the sea is getting rougher, it has deteriorated over the last few hours.
8:19pm Home Affairs Minister Jason Clare has told Channel 10 the situation north of Christmas Island is looking "increasingly grim", saying the chances of finding more survivors are decreasing:
Our planes are flying over at the moment they're seeing debris, they're seeing life jackets but unfortunately we haven't rescued anybody today that is still alive. We're reaching the end now of that 36 hour window where we've got the best chance of saving people, so it's looking increasingly grim.
7:55: Watch ABC News' recap of the situation:
7:40pm: Paul Power, from the Refugee Council of Australia, has told ABC News24 the situation is distressing for all involved:
6:40pm: On PM tonight Samantha Hawley spoke to Jo Meehan from AMSA, who says the rescue effort is likely to be scaled back tomorrow afternoon:
"Well our information suggests that possibly the conditions will remain good until tomorrow afternoon. So we will search all through the evening with slightly scaled down aviation search overnight and then ramp that back up to full-scale search for tomorrow."
"By tomorrow afternoon we'll have a look at what tomorrow morning's search has revealed and we will reassess at that point."
Ms Meehan says searchers are still hopeful of recovering survivors:
"It appears that survivability is good. We are encouraged by all of the survivors so far having life jackets and also there's a lot of debris in the region as well as some lifeboats that were deployed by the defence aircraft."
"So there are some options for survivors in the water to remain afloat."
6:16pm: West Australian Premier Colin Barnett has described the situation as a great human tragedy, and says the WA Coroner will conduct an inquiry into the deaths:
Because the survivors and sadly the bodies that are recovered will be taken to Christmas Island, that will fall within the jurisdiction of the West Australian Coroner.
[It's a] very sad situation, great human tragedy. And the West Australian Government is simply playing its role in supporting the search and rescue operation.
5:30pm: Matt Brown reports from Jakarta that Indonesian authorities have given conflicting accounts of how they responded to Australian requests to monitor the boat:
A spokesman for the Indonesian Navy, First Admiral Untung Suropati, says the Navy sent two small vessels to search for the asylum seeker boat on Wednesday morning.
While Australian authorities estimated it had been travelling slowly south from a spot about 38 nautical miles south of the Indonesian mainland, First Admiral Untung says the Navy headed for a spot 150 nautical miles from the coast.
As late as yesterday Indonesia’s national search and rescue agency said the Navy was still on its way to the scene of what, by then, had become a tragedy.
But First Admiral Untung has revealed the Navy’s vessels had already turned back because they encountered rough seas.
5:20pm: The ABC's Indonesia correspondent Matt Brown has obtained faxes sent between Australian and Indonesian rescue authorities, charting the the lead-up to the asylum seeker disaster:
See the faxes in full here.
4:30pm: An Iranian asylum-seeker in Indonesia has spoken with the ABC's Helen Brown in Jakarta of the fear he is feeling for a friend, who he believes was on the capsized vessel:
Masoud says his friend contacted him a few days ago and said he was going to try and reach Australia by boat.
He says the 41 year old felt it was the only option after living in Indonesia for one and half years, and having his application for refugee status denied.
"He said Masoud I go, you pray for me, and I hope if we go there you can follow us..”
Masoud says been trying to phone his friend since hearing about the search and rescue operation yesterday, but the phone keeps cutting out.
3:15pm: Independent MPs Tony Windsor and Rob Oakeshott have joined Dr Washer in calling for a bipartisan solution:
In a statement, Mr Windsor said both the Opposition and the Greens must take a fresh look at legislation put forward by Mr Oakeshott aimed at restoring offshore processing:
"Surely the real issue is about saving people's lives and the best way of doing this is to discourage people from getting on a boat in the first place."
"The boats are not safe - they are not cruise liners with life rafts and they are overcrowded.
"The Malaysia option would mean that people seeking asylum in Australia would not get onto a leaky boat in the first place."
Mr Oakeshott has singled out the Opposition, telling The Australian there was "a desire by some for toxic politics to win the day":
"It's really for, in my view [Opposition immigration spokesman] Scott Morrison, to start to think about what on earth he is doing on behalf of national policy by blocking this for political gain."
"[He is] absolutely sitting on his hands and saying it is not the Coalition's role to try and fix this; that this is somehow it is an impasse that is of the Government's making.
"If that is the position he is taking, get out of the way."
2:30pm: News Online chief political correspondent Simon Cullen has spoken with Opposition backbencher Mal Washer, who says the Coalition needs to consider supporting the Government's Malaysia solution:
"My party, the Coalition, and the Labor Party, after this tragedy, have really got to sit down again and think seriously through these issues as to how we could reduce this people smuggling business."
"There is no politics involved when it comes to this type of loss of life. I think the Coalition's got to reconsider all its options, and the Labor Party has to too."
Dr Washer says both sides need to be prepared to compromise, and the Malaysia deal should be part of the negotiations:
"The argument of course basically was how would these people be treated in Malaysia, and that's all got to be weighed up."
"But I would think they'd get treated pretty well if the Australian Government was monitoring this too.
"You've got to engage all countries in this to try to sort this out in a very cooperative framework because we do not want to see this loss of life again - it's a shame upon us to allow this to happen."
Read the full story here.
2:00pm: Home Affairs Minister Jason Clare has told Sky News surveillance planes have seen more bodies, but have not yet found any more survivors:
"They've also seen life jackets in the water, some floating on their own and some with people with life jackets, and unfortunately seen more bodies in the water this morning."
"So no good news - I can't report any information that they've seen people alive in the water at this time."
1:15pm: Sabra Lane spoke to AMSA spokesman Mal Larsen on The World Today:
"The search actually continued overnight, but obviously when first light commenced this morning it picked up in pace, because it is much easier to search for people in daylight."
"And a number of aircraft and vessels have been tasked and are on the scene, and are assisting authorities attempting to find survivors.
"I understand there are unconfirmed reports of sightings of bodies in the water. But obviously with such a sensitive issue, the authorities are very careful about obviously undertaking recovery activities and searching for survivors, and will release information as it can be confirmed.
"[In] that part of the world obviously the water is much warmer than for instance if it was in the Southern Ocean, so generally speaking survivability is increased. Obviously the conditions of the sea are a key point. What we do understand is that they are deteriorating."
Listen to the full audio here.
12:50pm: The ABC's Kerrin Binnie recaps the events of the past 24 hours:
12:05pm: The Department of Immigration and Citizenship is appealing for information about those on board the boat. Communications manager Sandi Logan tweets:
"If you know someone on board the capsized vessel near CI you can phone 1300 724 010 to provide information about them to #DIAC 8.30am-4.30pm."
12:02pm: After taking 96 of the asylum seekers to Christmas Island, HMAS Wollongong is now heading back to the search area to join four ships and five aircraft searching for more survivors.
11:52am: Prime Minister Julia Gillard says it is still possible that rescuers will find more survivors.
"We do face considerable loss of life at sea, but a search and rescue operation is underway right now. It is still possible for people to have survived and be in the water."
11:38am: The UN refugee agency has released a statement saying it is deeply concerned about yesterday's tragic boat accident:
"While the rescue effort is still under way, it appears that a number of people – presumed to be asylum-seekers – have lost their lives.
"This accident again underscores the dangerous nature of these hazardous journeys, and the desperate and dangerous measures people will resort to when they are fleeing persecution in their home countries.
"It also reinforces the need for renewed international solidarity and cooperation to find protection options for people that would help to reduce the need for these perilous journeys by boat.
"UNHCR calls on Australia and countries in the region to redouble their efforts to provide safer and more secure options for people to find protection other than through these dangerous and exploitative boat journeys.
"At this time, UNHCR expresses its appreciation for the rescue efforts being undertaken, and its solidarity and sympathy for the families and friends of those affected by this tragedy."
11:24am: Here's video of the asylum seekers arriving on Christmas Island.
11:10am: The ABC has the first footage of survivors arriving on Christmas Island.
11:00am: Ian Rintoul from the Refugee Action Coalition says the tragedy could have been averted if the Government had not been slow to react.
"On Wednesday they considered the boat to be in sufficient distress to tell it to turn around. They continued to get phone calls.
"It seems to me insufficient efforts had been made to find out the difficulties the boat was in and provide the support it was going to need."
10:45am: Christmas Island resident Mark Trenorden has sent the ABC a photo of the Cape Oceania, one of the merchant vessels called in to take survivors to safety. Send us your photos here.
10:30am: Christmas Island administrator Stephen Clay says a Navy vessel carrying 96 survivors arrived on the island in the early hours of the morning.
He says three have been admitted to hospital and the rest are being ferried to shore.
"They were transferred to the jetty, put into buses and transferred up to the Phosphate Hill immigration facility. They're getting medical checks up there. They appear calm and they were just sitting quietly."
10:20am: Richard Towle from the United Nations refugee agency says it is a time to reflect on the tragedy that arises from human desperation.
"They can't get on planes, they can't wait in orderly migration queues to find protection. They have to take whatever opportunities they can.
"Sadly and unfortunately, they have to resort increasingly to these dangerous journeys, whether its across land borders where they get exploited or whether its across sea borders, again to get exploited by smugglers."
10:10am: AMSA's Jo Meehan says the authority hopes to find more people now that the sun is rising. But conditions are getting worse.
"We have some deteriorating conditions. Unfortunately there are about two-metre swells and increasing to 20-knot winds with isolated showers. However, we do hope these won't hamper our efforts too much, we have information that water temperature is fair, so this is good news for survivability."
"Border Protection says the 110 survivors have arrived at Christmas Island."
9:45am: Here's audio of Home Affairs Minister Jason Clare's interview with AM's Sabra Lane.
9:25am: We've now gone almost 12 hours without hearing news of any more survivors.
9:15am: Liberal Senator Eric Abetz says the capsize is a tragedy.
"The boat tragedy off Christmas Island can be described as nothing else but a tragedy. It once again shows what occurs with the evil of people smuggling."
Labor Senator Doug Cameron also spoke about the incident.
"The Australian Navy are out there doing a fantastic job trying to save lives, rescuing refugees, they're out there picking bodies up. I just don't think it's an appropriate time to be pointing the finger at anyone and I hope that in the long term, we can get a more humane approach to refugee policy in this country."
8:33am: Here is the full audio of AM's interview with Christmas Island acting administrator Steve Clay.
8:23am: Here's the video of Home Affairs Minister Jason Clare addressing the media.
8:15am: Jason Clare told media the Australian Maritime Safety Authority's initial response was to tell the boat to return to Indonesia:
"When that phone call occurred on Wednesday morning, at about 1:30 in the morning, and [the boat] was 38 nautical miles south of Indonesia, AMSA told the people on that boat to return to Indonesia. That was very good advice then."
8:05am: Jason Om explains what Mr Clare had to say about what happened after the first distress call was sent out.
"He talked about the chronology of events. He said there were reports of a boat in distress earlier this week but it wasn't until about Wednesday morning when it was 38 nautical miles south of the Indonesian mainland where it was detected. It was the source of distress calls and AMSA got prepared to respond on that Wednesday night.
"But it wasn't until the Thursday morning that the concerns were increased about the safety of that boat and that's when border protection swung into action and the life rafts eventually were dropped off by an RAAF plane at about 5 o'clock on Thursday."
8:00am: Key points from Home Affairs Minister Jason Clare's media conference this morning:
- The Navy and merchant ships are still trying to pick up more survivors
- 109 adult men and one 13-year-old boy have been rescued and taken to Christmas Island
- A number had minor injuries but most were in good health
- The water temperature is 29 degrees and authorities believe people can stay alive for up to 36 hours if they have lifejackets or debris to hold on to
7:55am: Christmas Island's acting administrator Steve Clay has told AM that the island is preparing to treat survivors as they arrive.
"We are well prepared for whatever contingencies might arise. We've got medical staff to combine the local health services as well as OH&S (Occupational Health and Safety) which services immigration. So we've got a goodly number of doctors and nurses there.
"The other part is that we will deploy medical staff to those boats before people come off so that they get the right people off first.
"There is medical facilities at immigration ... [at] Phosphate Hill which is a community detention area. Not the same as the detention centre, it has medical facilities attached to it."
7:46am: Home Affairs Minister Jason Clare responds to a question about the earlier reports that two boats were believed to have been in distress.
"There was information that another boat was in distress, potentially, off the coast of East Timor. That search and rescue effort has now been called off. The information I have is that a report of a vessel in distress was received. We sent a Dash 8 out there to respond. The plane didn't locate any vessels that displayed any signs of distress. It appears a vessel had sent out an alert by pressing a beacon. But that vessel had no signs of distress."
7:44am: Jason Clare says Australian search and rescue authorities acted very proactively.
"As soon as we were given the information that there was a boat out there, we contacted Indonesian search and rescue authorities. We contacted AMSA, contacted customs and border protection authorities. Our planes flew over the area to identify where the boat was. It identified the boat that we think was in distress. It showed no visual signs of distress. But based on the information we've received, our boat and planes were pre-positioned to check and see if that boat was OK. As soon as we identified a capsized boat, Australian authorities took the action they did yesterday."
7:42am: Jason Clare says his focus is on finding more survivors.
"We're still in the critical window where more lives could be saved. The advice I have is that the water temperature is 29 degrees. People can survive out there for up to 36 hours if they have either lifejackets or they have debris to hold onto. That obviously is where my focus is right now."
7:40am: Jason Clare gives a chronology of what happened. No more survivors were found overnight. He says one of the survivors was a boy and the rest were all men.
"When the Dash 8 arrived on the scene yesterday afternoon we found around 40 people on top of the upturned hull and other people that were holding onto debris as much as 3 nautical miles away from the scene. There were lifejackets that were on the boat... And obviously the people that we've been able to pick up last night have been picked up by the merchant vessel as well as by our patrol boats that arrived on the scene.
"The information we have is that all the people on the boat were males. Except for one 13-year-old boy that has been rescued, all other people were all adults."
7:36am: Home Affairs Minister Jason Clare is addressing the media. He says the information he's providing "may change through the course of the day and through the course of the next few days."
7:28am: Here's the interview with the Australian Maritime Safety Authority's Jo Meehan from ABC News Breakfast:
7:13am: Home Affairs Minister Jason Clare is due to address the media from Sydney shortly with an update on the rescue efforts.
7:05am: The Australian Maritime Safety Authority says it cannot confirm that the boat Indonesia knew about on Tuesday was the same boat that capsized.
6:50am: Jo Meehan tells ABC News Breakfast that the search for survivors will continue today.
"Weather conditions seem to be moderate. We have 20 knot winds as well as some isolated showers. Today we are expecting two more defence vessels as well as four merchant vessels which have been directed to the scene. We will have to up to five aircraft doing some air surveillance throughout the day as well."
6:35am: Jo Meehan from the Australian Maritime Safety Authority says three bodies have been recovered and are being taken to Christmas Island.
"We have not recovered any further survivors over the search this evening but we can confirm we have three deceased. They have been recovered from the water and are on their way to Christmas Island with the survivors. We will continue to look for survivors for the rest of the day."
6:30am: Federal Opposition Leader Tony Abbott has told Channel 9 it is a tragic situation.
"It shows what a horrible business this whole people smuggling racket is. Obviously it's important we stop it one way or another but as I said I don't think today is a day for politics."
6:25am: Correspondent Helen Brown says Indonesia's coordinating agency for search and rescue spent most of yesterday believing two boats were in distress, but it now appears clear there was only one. Authorities say the boat was from Sri Lanka and first noticed on Sunday.
"Aust authorities say so far 3 men dead, 110 rescued from the asylum seeker boat which capsized nth of Christmas Island yesterday."
6:15am: From Jakarta, correspondent Helen Brown reports Indonesian authorities were confused by the information coming from Australia:
"An Australian surveillance aircraft spotted a people smuggling vessel in distress yesterday afternoon. However the Rescue Co-Ordination Centre sent Indonesian officials a telegram on Tuesday advising that a vessel carrying around 200 men had sought assistance, as there was damage to the hull and their boat was taking on water. The boat was advised that returning to Indonesia was the best course of action if the damage was significant. And that message was acknowledged. Indonesian officials say they asked all boats in the region to keep an eye out. But they also say they were confused by the information coming from Australia."
6:00am: After reports last night that two boats may have been at risk, this morning it appears clearer there is only one boat that the Australian Maritime Safety Authority is focusing on. It is still unclear where it has come from.
More from Julia Gillard's media conference at the Earth summit in Rio:
"The Minister for Home Affairs will make a comprehensive statement on the details of what has happened here in the morning, Australian time. The Acting PM will take responsibility for any national security arrangements that need to be made in Australia. I of course will keep in contact with both of them by telephone.
"I have had a brief conversation with President Yudhoyono about this matter. Our Indonesian and Australian personnel work well on search and rescue operations and all of our normal cooperative arrangement s will be brought to bear in this case.
"President Yudhoyono was of course distressed about the news. He assured me that we would work together, Indonesia and Australia, on the rescue efforts. We have good understandings between us and the best way of working together with these kind of incidents. I don't at this stage want to talk about policy or other questions. Our focus is on the search and rescue effort."
Home Affairs Minister Jason Clare will give an update at 7:15am AEST.
5:50am: Jo Meehan from the Australian Maritime Safety Authority says there is hope for more survivors as surveillance of the scene suggested people were wearing life vests.
A media release from AMSA gives details of the ships involved.
"The Australian Maritime Safety Authority will continue the search and rescue effort throughout the night, following the recovery of 110 survivors from a capsized vessel 120 nm south of Java, Indonesia.
"The survivors are currently being transferred to Christmas Island via HMAS Wollongong, WSA Dragon, JPO Vulpecula and Cape Oceania. The HMAS Wollongong will return to the scene to join the HMAS Larrakia and a number of aviation assets to continue searching for survivors overnight.
"Information on the condition of the vessel and the cause of the incident is still unknown."
5:45am: Three cargo ships, two navy vessels and aircraft have been searching the area throughout the night and into the morning.
Western Australia's Police Commissioner Karl O'Callaghan told the ABC says there are concerns a large number of asylum seekers may have drowned.
Prime Minister Julia Gillard has described the capsize as a tragic incident and said Australia was working with Indonesia to find more survivors.
"What is apparent is that there has been a large loss of life at sea. This is a very distressing and tragic incident. We don't know the full details yet, but clearly we have lost a number of lives in a very dangerous journey from Indonesia to Australia."
And as Indonesia correspondent Helen Brown reports, Indonesia remained uncertain about the source of the asylum seeker boat, how many people are involved and whether there are one or two boats.