A missing Indonesian submarine has been found, broken into at least three parts, deep in the Bali Sea, military officials said on Sunday, as the the nation's president sent condolences to relatives of the 53 crew.

Rescuers 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.