The official, who declined to be named, said the 37-year-old man had worked as a driver for a cargo company at Sukarno-Hatta airport, Jakarta's main airport for domestic and international flights.
The man, who had had no contact with sick fowl, died in early July, after being treated at three different hospitals, the official said. Tests had showed he was infected with the H5N1 strain of avian influenza.
The virus has infected 387 people in 15 countries, killing 245 of them, according to the World Health Organization's August 10 tally. Indonesia has the highest toll of any nation.
Although bird flu remains an animal disease, experts fear that the virus might mutate into a form easily passed from human to human, sparking a pandemic in which case millions could die.
(Reporting by Telly Nathalia; editing by Sara Webb and Roger Crabb)