The twin-engine Boeing 737 Max 8 took off from Jakarta's Soekarno-Hatta International Airport for the mining region of Pangkal Pinang early Monday.
The head of Indonesia's transportation safety committee (KNKT) said 69 hours of recorded data from 19 flights, including the one that crashed, had been downloaded successfully from a partly damaged flight data recorder recovered on Thursday.
Four ping locators - which are lowered into the sea to listen for the black box's signal - are now being used to locate the cockpit voice recorder after an additional unit was contributed by the U.S.
Few details have been released but the ministry said it had looked over half a dozen jets so far and discovered that one had a problem linked to its cockpit display while another had a glitch in a jet stabilisation system.
Syaugi paid tribute to a volunteer diver, Syahrul Anto, who died during the search effort on Friday.
Divers also retrieved two turbines and a wheel from the sea, Muhammed Syaugi said.
"We have heard a weak "ping". the divers are still searching for it", Syaugi said.
The plane is also reported to have experienced difficulties during a previous flight on Sunday from Bali to Jakarta.
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A forensic investigator collects samples of recovered belongings believed to be from the crashed Lion Air flight JT610.
Syaugi said a considerable amount of aircraft "skin" was found on the seafloor but not a large intact part of its fuselage as he'd indicated was possible Saturday.
He and other top officials including the military chief plan to meet with families today to explain the search operation.
While Lion Air said the condition of the aircraft before take-off had nothing to do with the fatal crash, airline safety analysts told AirlineRatings.com the two are "definitely linked".
In 2014, an AirAsia crash in the Java Sea during stormy weather killed 162 people.
President Joko Widodo encouraged rescuers to step the search for the dead, saying: 'I ask for you to use all your might, all the technology available, to work fast to find anything else'. The agency lifted the ban in 2016.The European Union similarly barred Indonesian carriers from flying into European airspace from 2007 until June.
The accident resurrected concerns about Indonesia's poor air safety record which until recently saw its carriers facing years-long bans from entering European Union and United States airspace.
Lion Air is one of Indonesia's youngest airlines but has grown rapidly, flying to dozens of domestic and worldwide destinations.