A missing Indonesian submarine has been found, broken into at least three parts, at the bottom of the Bali Sea, army and navy officials said on Sunday, as the president sent condolences to relatives of the 53 crew.

Rescuers also found new objects, including a life vest, that they believe belong 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 told reporters.

Navy chief of staff Yudo Margono said the crew were not to blame for the accident and that the submarine did not experience a blackout, blaming "forces of nature".

"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. "There are scattered parts of the submarine and its interior in the water."

President Joko Widodo earlier confirmed the discovery in the Bali Sea and sent the families of the victims his condolences.

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

A sonar scan on Saturday detected the submarine at 850 metres (2,790 feet), far beyond the Nanggala's diving range.

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

Navy officials said international help will be crucial in recovering the remains of the vessel.

Singapore Senior Minister Teo Chee Hean wrote on social media late on Sunday that a ROV (remotely operated vehicle) sent by the Singapore Navy was able to "recover a few critical items from the seabed at depth of more than 800 meters".

"We hope that this will help the families find some closure and certainty on the fate of their loved ones," he added.

Search teams said on Saturday they had found objects including prayer mat fragments near the submarine's last known location, leading the navy to believe the vessel had cracked.

Indonesia police said it would deploy teams to Bali and the Java town of Banyuwangi, which hosts the naval base from where the main search and recovery operations are being conducted, to help identify the victims once the bodies are retrieved.

Residents of Banyuwangi 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.

Southeast 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.