Tests by the World Health Organization showed that a 44-year-old man who died last week had the H5N1 virus, health ministry officials said.
Indonesia has registered more bird flu deaths this year than any other nation.
In contrast the outbreak in Vietnam now seems to be under control, due to a large culling and vaccination drive.
No Vietnamese deaths have been recorded in 2006.
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News Health Avian flu Bird flu H5N1 Pandemic Influenza Spanish Flu WHO Flu Indonesia