According to the director, the 44-year-old man, who died last week at a hospital in East Jakarta, had the H5N1 virus.
Two months ago, the biggest cluster bird flu in the world was found in Indonesia's North Sumatra province, followed by one in the province of Surabaya.
Bird flu has killed at least 132 people worldwide since it started ravaging Asian poultry stocks in late 2003, according to WHO.
(Source: IANS/Xinhua)