The flight data recorder was recovered by divers on Thursday in damaged condition and investigators said it required special handling to retrieve its information.
The cockpit voice recorder has not been recovered but searchers are focusing on a particular area based on a weak locator signal.
National Search and Rescue Agency chief Muhammad Syaugi said Sunday the search operation, now in its 7th day and involving hundreds of personnel and dozens of ships, would continue for another three days.
More than 100 body bags of human remains had been recovered. Syaugi said the number would continue to increase and remains were also now washing up on land.
He said weak signals, potentially from the cockpit voice recorder, were traced to a location but an object hadn't been found yet due to deep seabed mud.
Passengers on the Bali flight reported terrifying descents and in both cases the different cockpit crews requested to return to their departure airport shortly after takeoff.
Lion has claimed a technical problem was fixed after the Bali fight.
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.
The Lion Air crash is the worst airline disaster in Indonesia since 1997, when 234 people died on a Garuda flight near Medan. In December 2014, an AirAsia flight from Surabaya to Singapore plunged into the sea, killing all 162 on board. Indonesian airlines were barred in 2007 from flying to Europe because of safety concerns, though several were allowed to resume services in the following decade.
The ban was completely lifted in June. The US lifted a decadelong ban in 2016.
It has been expanding aggressively in Southeast Asia, a fast-growing region of more than 600 million people.