The 48-year-old had been searching for victims of the Lion Air flight, that plunged into the sea on Monday, 13 minutes after it took off from Jakarta.
Syachrul Anto had also been one of the main divers involved in the search for an Air Asia jet that crashed off Borneo in late 2014.
It is not yet clear how he died.
Muhammad Syaugi, head of Indonesia’s search and rescue agency, said: “Deepest condolences for the passing of a humanitarian hero from the Indonesian diving rescue team.”
The fatality came as the operation continued to recover human remains and pieces of the brand new Boeing 737 MAX 8.
So far 73 bodies have been recovered, but only four of the victims have been identified.
The search, taking place in around 100ft of water, has been hampered by strong currents and nearby pipelines.
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Divers have also been scouring the seabed for the cockpit voice recorder after a “low ping signal” was detected by a sonar locator.
Investigators are still trying to retrieve information from the damaged flight data recorder, recovered on Thursday, that could help determine the cause of the disaster.
The pilot of Monday’s Lion Air flight JT-610 had asked for, and received, permission to turn back to Jakarta.
The plane is also reported to have experienced difficulties during a previous flight on Sunday from Bali to Jakarta.
Lion Air has claimed a technical problem was fixed after Sunday’s flight.
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 Air Asia flight from Surabaya to Singapore plunged into the sea, killing all 162 on board.