The 22-year-old, who had a history of contact with dead poultry, died on Thursday at Jakarta's infectious diseases hospital, spokesman Ilham Patu said.
Local test results released on Wednesday confirmed the man had bird flu.
Blood and swab samples from the man have been sent to a World Health Organisation-approved laboratory in Hong Kong for confirmation.
If they come back positive, Indonesia will raise its death toll to 15.
Hundreds of millions of chickens and ducks have died or been culled since the H5N1 strain of bird flu started ravaging poultry stocks across Asia in 2003. It has also jumped to humans, killing at least 83 people in Asia and in Turkey.
Almost all the deaths have been linked to contact with infected poultry.