Muhammad Syaugi, head of the agency which is also known as Basarnas, told reporters at the port of Jakarta that divers had detected a characteristic "ping" sound from the second black box, Efenews reported.
"Although the sound is quite weak, it came from a spot not far from the ship 'Victory,'" he said, referring to a rescue vessel deployed to the area.
The brand new Boeing 737's other black box, or flight data recorder, had been found on Thursday, but so far investigators have not been able to recover any information from it, officials said.
Syaugi spoke at the dockside where Indonesian Navy officers could be seen lifting some heavy parts of the aircraft, such as its undercarriage.
"I haven't seen it myself but I got information from some divers that they have seen the fuselage," Syaugi said.
Flight JT-610 crashed into the Java Sea 13 minutes after taking off from Jakarta to fly to a neighbouring island on Monday. All 189 people on board were killed.
Meanwhile, Indonesian authorities also said one of the divers searching for the wreckage of plane died on Friday evening. The victim was identified as Syachrul Anto, a member of the Indonesian Diving Rescue Team.
National Search and Rescue Agency director Muhammad Syaugi said that the diver lost consciousness during the dive and died later at the Koja Regional Hospital in Jakarta.