The wreckage was found at a depth of 850 metres, and had broken into three pieces.

This article was updated on April 25.

Worst-case fears over the fate of an Indonesian submarine that went missing with 53 crew members on board were realised on Sunday as the wreckage of the sunken sub was located. Indonesia military commander Air Chief Marshal Hadi Tjahjanto said Sunday that the sub had been located and confirmed all crew members had perished.

The German-built KRI Nanggala 402 was scheduled to conduct live torpedo exercises early on Wednesday when it asked for permission to dive. It lost contact shortly after.

An oil spill located where the vessel was thought to have submerged during those exercises initially fuelled fears that the Southeast Asian nation had become the latest country to suffer a fatal submarine disaster.

Navy spokesman Julius Widjojono said Thursday that search teams were focused on an area around the oil slick, but that the exact location of the vessel had yet to be pinpointed at that time.

The news of the wreckage being located came a day after debris believed to be from the KRI Nanggala-402 submarine was found floating about two miles (3.2 km) from the submarine’s last known location in the Bali Strait, leading military officials to change the vessel’s status from ‘missing’ to ‘sunk.’

Indonesia’s Rigel warship scanned the area with sonar, which uses sound waves to locate objects, and a magnetometer to search for the submarine’s steel superstructure, Tjahjanto told a news conference. Following a suspected location of the stricken sub, the MV Swift rescue ship from Singapore then sent a remote operated vehicle to the sea floor to get clearer underwater visual imagery, he said.

The submarine asked for permission to dive, or submerge, at 3 a.m. local time Wednesday before losing contact, authorities said. Margono said the submarine had just fired two torpedoes — one with real ammunition and another with a practice warhead — as part of training exercises in the Bali Strait, a stretch of water between the islands of Java and Bali that connects to the Indian Ocean and Bali Sea.

In breaking the tragic news, Tjahjanto extended his deepest condolences to the families of the crew, known as the Golden Shark unit, and said all those on board would be given honours and an increase in rank.

He also noted that the Indonesian government will work with the International Submarine Escape and Rescue Liaison Office, given the depth of the wreckage, “because to evacuate the Nanggala submarine we need international cooperation.”

The International Submarine Escape and Rescue Liaison Office (ISMERLO), an organisation that facilitates an international response for distressed submarines.

The 1,395-ton KRI Nanggala-402 was built in 1977 by the German shipbuilding company Howaldtswerke-Deutsche Werft (HDW) and joined the ranks of the Indonesian Navy in 1981, according to a ministry statement.

The submarine underwent a two-year refit in South Korea that was completed in 2012, according to the Indonesian cabinet secretariat.

(News from AFP, CNN, and wire services)