Special ships and remotely operated underwater vehicles had been deployed following Monday's crash to search for the plane's hull and flight recorders.
Indonesian divers resumed a search on Tuesday for an airliner that crashed with 189 people on board, as "pinger locators" tried to zero in on its cockpit recorders and uncover why an almost-new plane went down in the sea minutes after take-off.
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".
"We're going to see it ourselves on location and hopefully that is the main body of the plane that we've been looking for".
Indonesia's air travel industry is booming, with the number of domestic passengers growing significantly over the past decade, but it has acquired a reputation for poor regulation and its airlines had previously been banned from U.S. and European airspace.
Muhammad Syaugi told reporters Wednesday that the search effort is battling strong currents but they remain confident the aircraft hull will be found.
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Indonesian TV broadcast a smartphone video of passengers boarding Flight 610, its mundane details transformed into unsettling moments by knowledge of the tragedy that would transpire.
While there is no sign of survivors, rescuers have recovered some bodies and personal items, including baby shoes, the report said.
The Ministry of Transportation has earlier ordered the suspension of several members of Lion Air's management, including its director of maintenance and engineering, quality control manager and an aircraft release engineer, so they can assist in the accident investigation.
Searchers show IDs and photos found in the water after the Lion Air JT 610 plane crashed. At one point, the passenger who shot the video, Paul Ferdinand Ayorbaba, zooms in on his boarding pass.
However, he ordered the inspection of eight aircraft of the same model now being operated by Lion Air, and one operated by Garuda Indonesia.
The Boeing 737 Max 8 passenger plane was flying from Jakarta to Pangkal Pinang at 06.10 local time (2330GMT Sunday) but lost contact with the air traffic controllers about 13 minutes after it took off.
"Based on the presentation of the head of the National Search and Rescue Agency, the coordinates of the suspected body of the aircraft have been found".
Indonesian airlines were banned from flying to the United States in 2007 because they were "deficient in one or more areas, such as technical expertise, trained personnel, record-keeping, or inspection procedures", the Federal Aviation Administration said.