Ground staff lost touch with flight JT610 of Indonesian budget airline Lion Air 13 minutes after the Boeing 737 MAX 8 took off early on Monday from Jakarta, on its way to the tin-mining town of Pangkal Pinang.
There were no survivors.
Indonesia's military chief said he believed the plane had been located, and a transport safety official said divers would be sent to confirm the origin of a "ping" signal picked up by a search and rescue team late on Tuesday.
"We strongly believe that we have found a part of the fuselage," armed forces chief Hadi Tjahjanto told broadcaster TV One.
Speaking on board the navy ship KRI Rigel, navy official Colonel Haris Djoko Nugroho told broadcaster TVOne that a 22-metre long object had been found in waters about 32 metres deep, and a sonar was being used to identify it.
Divers would also be sent to check, he said.
The Rigel has been searching in an area about 5 nautical miles from the site where the aircraft lost contact.
The plane's blackboxes, as the cockpit voice recorder and flight data recorder are known, should help explain why the almost-new jet went down minutes after take-off.
Although it is now almost certain that everyone on the plane died, relatives are desperate to find traces of their loved ones. Only body parts and debris have been found.
Investigators are looking into why the pilot of the downed aircraft had asked to return to base shortly after take-off, a request that ground control officials had granted, although the flight crashed soon after.
An official of the national transport safety panel has said the plane had technical problems on its previous flight on Sunday, from the city of Denpasar on the resort island of Bali, including an issue over "unreliable airspeed".
The accident is the first to be reported involving the widely sold Boeing 737 MAX, an updated, more fuel-efficient version of the manufacturer's single-aisle jet.
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Privately owned Lion Air, founded in 1999, said the aircraft, had been in operation since August and was airworthy, with its pilot and co-pilot having 11,000 hours of flying time between them.
The airline is to meet a team from Boeing on Wednesday to discuss the fate of its 737 MAX 8 plane.
"We have many questions for them," Lion Air Director Daniel Putut told reporters on Tuesday.
"This was a new plane."
(Additional reporting by Jakarta bureau Editing by Michael Perry, Robert Birsel)
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