Flight JT 610 sped up as it suddenly lost altitude and then vanished from radar 12 minutes after take-off, with authorities saying witnesses saw the jet plunge into the water.
While search teams have found some debris and remains of passengers, they were still searching for the fuselage of the plane as well as the crucial black box recorders, which may help explain flight JT610's mysterious crash.
Lion Air has acknowledged that the twin-engine jetliner had also experienced a technical problem during its previous flight, from Bali to Jakarta on Sunday, though maintaining that it was "resolved through maintenance procedures issued by the aircraft's factory".
"We haven't downloaded the data because there are some broken parts in the black box", Haryo Satmiko, the deputy of the transport safety panel, said of the flight data recorder found on Thursday, adding that some of the damage was to a socket on the device.
The minister also said fares provided by low-cost carriers will be evaluated, saying they are frequently too low and excessive cost-cutting could indirectly affect flight safety.
The airline is to meet a team from Boeing this morning to discuss the fate of its 737 MAX 8 plane.
A pitot tube is a small tube on the wings or fuselage of an aircraft that determines critical information like altitude and air speed.
On Wednesday, officials said they thought the plane had been located and were trying to confirm the origin of a "ping" signal picked up the previous day.
The data recorder was reportedly found in almost 100 feet of water about 1,600 feet from where the jet lost contact.
It was the worst airline disaster in Indonesia since 1997 and renewed concerns about safety in its fast-growing aviation industry, which was recently removed from European Union and U.S. blacklists.
Earlier, a navy official said Indonesian search and rescue workers have detected a 22-metre long object underwater in the area where the passenger jet with 189 people on board crashed.
A spokesman said the European Commission had no immediate plans to renew the ban on Lion Air, but the Australian government warned its officials and contractors not to fly on Lion Air pending findings from the crash investigation.
Indonesia has deployed "pinger locators" in the hunt for the plane's blackboxes, as the cockpit voice recorder and flight data recorder are known, at the crash site.
Lion Air has ordered 50 of the MAX 8 planes and one of its subsidiary airlines was the first to operate the new generation jet a year ago.
Video of passengers boarding the flight has been broadcast on Indonesian TV.
Six body parts had been filled with body parts already recovered. The ban was completely lifted in June.
Lion Air is one of Indonesia's youngest airlines but has grown rapidly, flying to dozens of domestic and worldwide destinations. Local airline traffic more than tripled between 2005 and 2017 to 97 million people, according to the CAPA Center for Aviation, and is dominated by flag carrier PT Garuda Indonesia and Lion Air Group.