A missing Indonesian submarine has been found, broken into at least three parts, deep in the Bali Sea, as the president sent condolences to relatives of the 53 crew.

Army and navy officials said rescuers found new objects, including a life vest, that they believe belonged to those aboard the 44-year old KRI Nanggala-402, which lost contact on Wednesday as it prepared to conduct a torpedo drill.

“Based on the evidence, it can be stated that the KRI Nanggala has sunk and all of its crew have died,” military chief Marshal Hadi Tjahjanto said on Sunday.

Navy chief of staff Yudo Margono said the crew were not to blame for the accident.

“The KRI Nanggala is divided into three parts, the hull of the ship, the stern of the ship, and the main parts are all separated, with the main part found cracked,” he said.

Indonesian President Joko Widodo has said he had sent his condolences to the families of the 53 crew.

“The army and navy have changed the status of the KRI Nanggala 402 submarine from having lost contact to being ‘sub-sunk’ or drowned,” Mr Widodo said.

An image of the vessel on the sea floor. Photo: AAP

“All of us Indonesians express our deep sorrow over this tragedy, especially to the families of the submarine crew.”

“Based on the evidence, it can be stated that the KRI Nanggala has sunk and all of its crew have died,” Mr Tjahjanto said.

The submarine’s grave on the Bali sea floor. Photo: AAP

Search teams said on Saturday they had found objects including prayer mat fragments and a bottle of periscope lubricant near the submarine’s last-known location, leading the navy to believe the vessel had cracked.

Mr Margono confirmed a sonar scan had detected a submarine-like object at 850 metres, beyond the Nanggala’s diving range.

More than a dozen helicopters and ships were searching the area where contact was lost, with the United States, Australia, Singapore, Malaysia, and India providing assistance.

Australia sends condolences

Prime Minister Scott Morrison contacted Mr Widodo to express the nation’s sympathies.

“A tragic reminder of the ultimate sacrifice our service people make for their country. It was an honour to contribute to search efforts. Australia stands by you in your time of loss,” Mr Morrison said.

Residents of the East Java town of Banyuwangi, which hosts the naval base from where search-and-rescue operations are being conducted, joined nationwide calls to accelerate the modernisation of Indonesia’s defence forces.

“This can be a learning point for the government to advance its military technology and be careful in how it uses its (existing) technology because its people’s lives are at stake,” said 29-year-old resident Hein Ferdy Sentoso.

A life jacket found in waters during a search for the Indonesian Navy submarine. Photo: AAP

South-East Asia’s most populous country has sought to revamp its military capability, yet some equipment is still old and there have been fatal accidents in recent years.

Indonesia had five submarines before the latest accident: Two German-built Type 209s including Nanggala and three newer South Korean vessels.

-AAP