Divers have located parts of the wreckage of Sriwijaya Air Flight SJ182 and have collected the black boxes.
The Cockpit Voice Recorder and Flight Data Recorder were found in two locations on the seabed, said Suryanto Cahyono, head of the National Transportation Safety Commission.
The Boeing 737-500 departed from Jakarta en route to Pontianak on Saturday, but crashed into the sea within minutes of take-off.
It lost 10,000 feet in less than a minute before abruptly disappearing from radar.
The main fuselage section still remains on the seabed but body parts have been recovered by Navy divers.
The US National Transportation Safety Board has sent an aircraft crash expert to assist with the investigation.
The crash site is close to Laki Island in the Pulau Seribu (Thousand Island) archipelago just 20 miles north of Jakarta, which is a popular weekend holiday spot for the city’s residents.
The plane was carrying 50 passengers and a dozen crew members, Indonesia’s Minister of Transportation Budi Karya Sumadi said.
Officials are keeping tight-lipped about the possible cause of the accident until flight data and voivce recordings are fully analysed.
Indonesia has a patchy air safety record and has suffered numerous air accidents in recent years.
It includes the Lion Air Boeing 737 Max 8 crash, which was put down to Boeing’s malfunctioning software.
In 2014, an Indonesian AirAsia plane crashed into the Java Sea, killing 162 people.
Written by Ray Montgomery, Asia Editor
