The bodies of up to 60 asylum seekers who drowned off Christmas Island will be left in the water, with Australian authorities deciding their retrieval is not a priority.

While an investigation has been launched into the several delays it took to begin a full-scale search after the boat was first spotted on Wednesday afternoon, Australian Customs and Border Protection (ACBP) have decided not to retrieve the bodies.

“No attempts to recover the deceased will be made today,” a spokeswoman said.

“Vessels and aircraft are involved in a range of high priority operations in the waters near Christmas Island and elsewhere.

“Our priority in these operations remains the protection of life, responding to water rescues which may prevent any further loss of life.”

The ACBP may try to recover the bodies at a later date, but the spokeswoman said the likelihood of “successful recovery” diminished over time.

When asked if the home affairs minister, Jason Clare, agreed with the decision, a spokesman said it was an operational decision.

Refugee advocates have expressed dismay that bodies will be left in the ocean, saying the asylum seekers deserved some dignity.

Refugee Action Coalition spokesman Ian Rintoul said retrieving the bodies would be a comfort to the families left behind.

“We’re always in favour of retrieving their bodies. There are families in refugee communities who look at these episodes with anguish and it can provide closure to get a better idea of who was on the boat and letting people know what has happened to relatives and loved ones,” he said.

Rintoul said the nationalities of people on the boat should emerge over the next few days when families and friends do not hear from those who should have arrived at the island.

He also criticised the time it took for a proper search to be launched, saying it was almost two days after the boat was first seen.

“When the plane first spotted the boat it was stationed in the water, that in itself should have set off alarm bells for people in that plane and the rescue authorities,” he said.

“These kind of boats when they are in the water and stationary are unstable.

“That boat was only a few hours, at the most, from arriving at Christmas Island – when it did not arrive it should have set off immediate alarm bells for a wider search. But all we saw was a navy boat.

“There was no mayday call until Friday. There is clearly a need for an inquiry into this particular boat in distress and we need to know the protocol and procedures the navy and rescue authorities were operating in.”

The boat was first noticed by an air force plane on Wednesday afternoon about 52km north of Christmas Island. It did not appear to be in distress, but it was not moving.

The crew of the plane counted 55 people on deck. Most of the asylum seekers were men but women and children also appeared to be on board.

A navy ship was sent out about seven hours later to intercept the boat and arrived where the boat was last seen upright in the early hours of Thursday morning.

The Australian Maritime Safety Authority did not send out a PAN-PAN (Potential Assistance Needed) call until 10am on Friday. The capsized boat was not found until Friday afternoon.

Rintoul said as far as the refugee advocates had been told, only a corridor of sea was searched on Thursday and he wanted a far-reaching inquiry, not just the standard investigation which was taking place.

“We’ve got a situation where there simply has not been an adequate response,” he said.

Phil Glendenning, from the research and awareness organisation the Edmund Rice Centre, said he supported Rintoul’s calls for a full investigation into the timeframe of the search and said the bodies should not be left in the ocean.

“This is an unmitigated tragedy of every proportion,” he said.

“Our preference would be retrieving the bodies so they can be given the chance of a dignified farewell without putting lives at risk.

“We also need to make sure this does not happen again.

“... a bipartisan effort needs to be made to assist people to be processed safely and securely. They need to be protected, not punished.”

The search was called off on Sunday night with no survivors found and the discovery of 13 bodies.

Border Protection Commander Rear Admiral David Johnston said on Sunday none of the bodies spotted in the search were pulled from the water.

"The recovery of bodies is complex and time-consuming, so all the surface vessels are continuing [the search] because it remains possible that there are survivors in the water," he said.

Two planes and two ships searched for survivors from Friday until Sunday night.

Clare said the search would be the subject of a standard review by Customs and Border Protection.