"We dug and we got the black box", a diver, identified as Hendra, told broadcaster Metro TV on board a search vessel, the Baruna Jaya, describing how his team found the orange-colored box intact in debris on the muddy sea floor.
The crash renewed concerns about safety in Indonesia's fast-growing aviation industry.
"We are prioritising finding the main wreckage of the jet using five warships equipped with sonar to detect metal underwater", said Yusuf Latif, spokesman of the Indonesian search and rescue agency.
Soerjanto Tjahjono, Chief of Indonesia's transportation safety committee, said Wednesday that they are "70% sure" the pings are from flight 610's flight data recorder.
Indonesia showed images of divers retrieving an orange device, which is thought to house the flight data and cockpit voice recorder, collectively known as the "black box".
Lion Air, Indonesia's biggest budget airline which has been engaged in huge expansion, announced earlier this year it was buying 50 Boeing-737 MAX 10 jets for US$6.24 billion.
National Search and Rescue Agency (Basarnas) chief Muhammad Syaugi said the current was so strong that it had shifted a large ship, while efforts were further complicated because of oil and gas pipelines in the vicinity.
Late yesterday, Indonesia's Transport Minister said the technical director of Lion Air and staff who approved Monday's flight had been removed from duty by the ministry.
The crash is the first one involving the Boeing 737 MAX 8, a new fuel-efficient version of the legendary passenger jet.
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.
Police officer Hudi Suryanto said forensic doctors had identified only one victim, Jannatun Cintya Dewi, 24, based on her fingerprints.
Data from flight-tracking sites show the plane had erratic speed and altitude in the early minutes of a flight on Sunday and on its fatal flight Monday.
In a statement, the company offered its "heartfelt sympathies" to the victims and their loved ones, and said it was providing technical assistance at the direction of government authorities investigating the incident.
"About three to eight minutes after it took off, I felt like the plane was losing power and unable to rise", Soetanto said, per the AP.
Its 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. The US lifted a decadelong ban in 2016.
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