The German-built KRI Nanggala 402 was scheduled to do live torpedo exercises when it asked for permission to dive early yesterday morning, authorities said.
“After permission was given according to the procedure, the submarine lost contact and could not be reached,” the defence ministry said.
A helicopter looking for the missing vessel spotted an oil spill in waters where the submarine was thought to have submerged, it added.
The navy said it has not pinpointed the submarine’s location but narrowed the search down based on the spill.
The oil “could indicate damage on the body” of the submarine, navy spokesman Julius Widjojono told MetroTV.
Two warships and some 400 personnel were sent out to hunt for the sub, while a third vessel was deployed from the capital Jakarta.
The navy also sent out an international distress signal and “several countries have responded and are ready to help including Singapore, Australia and India,” the defence ministry said.
There were 53 crew aboard the vessel, which was believed to be in waters about 700 metres (2,300 feet) deep.
Indonesia, which has been moving to upgrade its military equipment in recent years, has five German and South Korean-built submarines in its fleet.
The 1,300-tonne KRI Nanggala 402 was built in 1978, according to a government website.
The vessel is a Type 209 diesel-electric attack submarine that has served in more than a dozen navies around the world, including Greece, India, Argentina and Turkey, over the past half century.
“It’s a classic submarine,” French navy vice admiral Antoine Beaussant told AFP.
It had a safety descent level of 250 metres, and “if it went down to rest at 700 metres the likelihood is it would have broken up,” he said.
While the Southeast Asian archipelago has not previously suffered a major submarine disaster, other countries have been struck by accidents in the past.
Among them was the 2000 sinking of the Kursk, the pride of Russia’s Northern Fleet.
The submarine was on manoeuvres in the Barents Sea on August 12, 2000 when it sank with the loss of all 118 aboard. An inquiry found a torpedo had exploded, detonating all the others.
Most crew died instantly but some survived for several days - with a few keeping heart-breaking diaries written in blood to their loved ones - before suffocating.
Seventy Chinese naval officers and crew were killed, apparently suffocated, in an accident on a Ming-class submarine conducting exercises in 2003.
In 2008, 20 people were killed by poisonous gas when a fire extinguishing system was accidentally activated on a Russian submarine being tested in the Sea of Japan.
In 2018, authorities found the wreckage of an Argentine submarine that had gone missing a year earlier with 44 sailors aboard.
Crushed from an implosion, the ARA San Juan was located at a depth of more than 900 metres (3,000 feet) in an area of undersea craters and canyons 400 kilometres (250 miles) off the coast of Argentina.
In 2019, a French submarine that had gone missing in the Mediterranean more than 50 years earlier was found.
The diesel-electric Minerve submarine was lost off France’s southern coast with 52 sailors on board on January 27, 1968.
Experts believe that the disaster was caused by a problem with the Minerve’s rudder, a collision with another boat, the explosion of a missile or torpedo, or a fault with its oxygen supply systems.