Helicopters also flew from Bali at first light.
Officials have said the air supply of the submarine, which had been cleared for use and was said to be in good condition, would last only until Saturday.
"Hopefully before they can be found, the oxygen will be enough," Yudo Margono, the navy chief of staff, told a news conference.
The commander of the Indonesian submarine fleet, Harry Setiawan, was one of four people aboard who were not regular crew members, a military official said.
While nothing conclusive had been found in the search so far, Yudo said an item with "high magnetic force" at a depth of 50-100 metres (164-328 ft) had been spotted. It was unclear if the object was suspended or on the sea floor.
The diesel-electric powered submarine could withstand a depth of up to 500 metres but anything more could be fatal, a navy spokesman said. The Bali Sea can reach depths of more than 1,500 metres.
An aerial search also spotted an oil spill near the submarine's dive location, which the navy said could indicate damage to the vessel or could be a signal from the crew.
The 1,395-tonne vessel was built in Germany in 1977 and joined the Indonesian fleet in 1981, according to the defence ministry. It underwent a two-year refit in South Korea that was completed in 2012.
The navy has said a blackout may have occurred during static diving, causing a loss of control and preventing emergency procedures from being carried out.
U.S. SENDS "AIRBORNE ASSETS"
A number of countries have responded to Indonesia's requests for assistance, with Australia, Malaysia, India, Singapore and the United States sending specialised ships or aircraft.
The U.S. Defence Department is sending "airborne assets" to assist in the submarine search, Pentagon spokesman John Kirby said on Twitter.
U.S. Defence Secretary Lloyd Austin is scheduled to speak with Indonesian Defence Minister Prabowo Subianto on Friday "to convey our sorrow and to discuss how else the United States can be of assistance," Kirby said.
Meanwhile, two Australian ships were heading for the search area including a support ship and a frigate with sonar capabilities, the defence department said in a statement.
Indonesia has been seeking to modernise its defence capabilities but some of its equipment is old and there have been fatal accidents in recent years.
Indonesia in the past operated a fleet of 12 submarines bought from the Soviet Union to patrol the waters of the sprawling archipelago.
It now operates five - the two German-built Type 209 submarines and three newer South Korean vessels.
(Additional reporting by Agustinus Beo Da Costa and Ajeng Dinar Ulfiani in Banyuwangi Colin Packham in Canberra and Idrees Ali in Washington; Writing by Ed Davies; Editing by Stephen Coates) ((Ed.Davies@thomsonreuters.com;))