Local tests, which are usually accurate, show that a 16-year-old boy died of the disease on Monday night, health ministry officials said.
Indonesia has registered more bird flu deaths this year than any other nation.
Vietnam has also been badly affected, suffering 42 deaths, but the outbreak there seems to be under control.
No one has died from the disease in Vietnam since the beginning of 2006.
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News Health Avian flu Bird flu H5N1 Pandemic Influenza Spanish Flu WHO Flu Indonesia