The aircraft suffered a technical problem on a flight from the resort island of Bali to Jakarta on Sunday night but it was "resolved according to procedure", Edward Sirait, chief executive of Lion Air Group, told reporters.
Passengers on the Sunday flight from Bali to Jakarta have recounted problems that including a long-delayed take-off for an engine check and terrifying descents in the first 10 minutes in the air.
Furthermore, the National Transportation Safety Commission (KNKT) rescue team successfully recovered the aircraft's flight data recorder (FDR) from the plane's wreckage submerged under the seabed just 500 meters from its last contact with ATC.
President Joko Widodo had also ordered a review of all regulations relating to flight safety, Sumadi said.
Indonesian rescuers said that the Boeing crash there were no survivors. Specialist ships and remotely operated underwater vehicles have been deployed to search for the plane's hull and flight recorders.
A team from the U.S. National Transportation Safety Board including Boeing experts has joined the Indonesian investigation.
A pitot tube is a small tube on the wings or fuselage of an aircraft that determines critical information like altitude and air speed.
The plane, which had only been in service since August, went silent 13 minutes after taking off on Monday from Jakarta, heading for the tin-mining town of Pangkal Pinang.
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"Now we are finding bigger parts as opposed to only small debris yesterday", Syaugi said.
But pilot and engineering sources told Reuters the FlightRadar24 data for both flights, while not conclusive, could be a potential indicator of something wrong with the pitot-static systems.
Military chief Hadi Tjahjanto said that divers had already gone down to check the location from where the signal was picked up by a search and rescue team late on Tuesday, but were contending with strong currents.
Meanwhile, on November 1, Thursday, the transport ministry of Indonesia directed Lion Air to immediately suspend the company's director of maintenance, managers in charge of quality control and fleet maintenance, as well as the engineer who cleared the plane for flight despite reported technical issues, in order to ensure an unhampered investigation.
The pilot and co-pilot had more than 11,000 hours flying time between them and had undergone recent medical checkups and drug testing, the carrier said.
Efforts are now focused on retrieving the second of the two black boxes, as the cockpit voice recorder and the flight data recorder are known, the head of Indonesia's transport safety panel said.
The crash is the worst airline disaster in Indonesia since an AirAsia flight from Surabaya to Singapore plunged into the sea in December 2014, killing all 162 on board. It is assumed that this part can be a body of the aircraft, reports our site.
Lion Air is one of Indonesia's youngest airlines but has grown rapidly, flying to dozens of domestic and worldwide destinations.
Indonesia is one of the world's fastest-growing aviation markets.