Indonesian President Joko Widodo said on Sunday the country's missing submarine had been found sunken in the Bali Sea and that 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," he told reporters.
"All of us Indonesians express our deep sorrow over this tragedy, especially to the families of the submarine crew."
The 44-year old KRI Nanggala-402 lost contact on Wednesday as it prepared to conduct a torpedo drill.
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.
Navy Chief of Staff Yudo Margono said on Saturday that 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 are searching the area where contact was lost, with the United States, Australia, Singapore, Malaysia, and India providing assistance.
Residents of the East Java town of Banyuwangi, which hosts the naval base from where search and rescue operations are being conducted, told Reuters they sympathised with the victims' families.
Indonesia had five submarines before the latest accident: two German-built Type 209s including Nanggala and three newer South Korean vessels.