Nyoman Kandun, a director general at the ministry, said the 15-year-old boy from Tasikmalaya in West Java had had contact with poultry.
Indonesia has seen a steady rise in the number of human infections and deaths since its first known outbreak of H5N1 in poultry in late 2003. It has infected 48 Indonesians so far.
Authorities have sent samples from a seven-year-old Indonesian girl who also died week to a WHO-accredited laboratory in Hong Kong after she tested positive for bird flu locally.
Bird flu remains essentially an animal disease but climbing human deaths have put many countries around the world on alert for fear it may mutate into one that could pass easily among people and trigger a pandemic, killing millions.
Indonesia drew international attention last month when the virus killed as many as seven members of a single family in North Sumatra. Experts said there could have been limited human-to-human transmission in this cluster case.
But they stressed genetic analyses of the virus has not shown all of the traits that are known so far to allow it to spread easily among people.
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