The Boeing 737-500 aircraft plunged into the Java Sea with 62 people on board shortly after taking off from the Soekarno-Hatta International Airport near Indonesia’s capital on Saturday.
Authorities have narrowed down the approximate location of the black boxes, after picking up signals from the devices, which record information about the speed, altitude, and direction of the plane as well as flight crew conversations.
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But the search has been hindered by the tons of plane debris and layers of sea mud underneath which the boxes may be buried in waters about 23 meters (75 feet) deep.
The recordings could prove crucial to understanding what caused a catastrophic loss of control after take-off.
While the remote-controlled vehicles scoured the seabed, navy vessels with sonar searched from the surface.
Once the black boxes are retrieved, Indonesia's National Transportation Safety Committee (KNKT) expects to be able to read the information in three days.
About 160 divers are part of the 3,600 personnel involved in the search operation.