The Indonesian military could not immediately be reached for comment, and the Australian and Singaporean militaries did not immediately respond to requests for comment.
Indonesian National Armed Forces Commander Marshal Hadi Tjahjanto told national paper Kompas that the submarine disappeared in waters about 60 miles (95 kilometers) north of the island of Bali at about 3 a.m. local time.
Tjahjanto said the navy has deployed scores of ships to search the area, including a hydrographic survey ship, and has asked for help from Singapore and Australia, which have submarine rescue vessels.
Indonesia's navy is searching for a submarine with 53 people on board that lost contact on Wednesday and is seeking help from neighbouring Australia and Singapore in the hunt, the Indonesian military chief told Reuters.More news: DOJ To Investigate Minneapolis Police For Possible Patterns Of Excessive Force
The 42-year old German-made submarine, KRI Nanggala-402, is part of the Indonesian Navy's 2nd Fleet and was taking in naval drills that were supposed to culminate on Thursday.
The Defense Ministry said in a statement that the submarine lost contact after being granted clearance to dive.
It said it believes the submarine sank to a depth of 600-700 metres (2,000-2,300 feet). In 2017, an Argentine military submarine went missing in the southern Atlantic with 44 crew on board.
The KRI Nanggala-402 submarine stopped responding in the early morning defense officials said.More news: Trudeau asks Atlantic premiers to help with Ontario COVID-19 outbreak
'We don't know yet whether the communication equipments were broken or the submarine has sunken. It underwent a two-year refit in South Korea that was completed in 2012.
According to the Daily Star, which cites the country's military chief, the missing vessel is one of five submarines in the Indonesian Navy.
It plans to operate at least eight by 2024.
In 2015, an Indonesian military transport plane crashed into a northern residential area two minutes after takeoff, killing more than 100 people.More news: Signs discouraging travel into B.C. to be posted along Alberta border