There are concerns that the vessel, which was holding 53 crew members, could have already sunk to a depth where it may have been crushed.
The KRI Nanggala 402 went missing during exercises off the coast of Bali on Wednesday, prompting a desperate hunt for the missing vessel.
Australia, India, Malaysia and Singapore have so far sent assistance. A US Navy P-8 Poseidon aircraft landed in Bali early on Saturday morning.
“Indonesia is a good friend and strategic partner. We were all deeply saddened to see the reports about their submarine and our thoughts and our prayers are with the Indonesian sailors, the Indonesian navy, and of course all their families,” said Pentagon spokesman John Kirby.
An oil slick where it was thought to have submerged suggested damage to a fuel tank may have been a factor.
The Indonesian military said late on Thursday night that it had detected signs of an object at a depth of between 50 and 100 metres and had deployed ships with sonar-tracking equipment in the hope it was the KRI Nanggala 402.
A military spokesman said the submarine would only have enough oxygen to last until around 3am local time on Saturday. That deadline has now passed.
The quest has since included at least six vessels, a helicopter, and 400 soldiers. Singapore and Malaysia have sent ships to the area.
On Wednesday morning, the KRI Nanggala 402 lost touch shortly after seeking permission to dive during live torpedo drills. The submarine was constructed in Germany and is one of five that Indonesia operates. It was built in the late 1970s and undergone a two-year refit in South Korea, which was finished in 2012.
According to a navy spokesman, this is the first time Indonesia has lost one of its submarines. However, related events have occurred elsewhere.
The Kursk, a Russian navy sub, sunk during manoeuvres in the Barents Sea in 2000, killing all 118 crew members. An investigation revealed that one torpedo detonated, detonating all the others. The majority of the Kursk’s crew died immediately, but others survived for several days before succumbing to suffocation.
In 2003, 70 Chinese naval officers and crew were killed during drills on a Ming-class submarine.
In 2017, an Argentine military submarine with 44 crew members went missing in the southern Atlantic. A year later, the wreckage was discovered, and authorities claimed that the submarine had imploded.