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 human infections and deaths since its first known outbreak of H5N1 in poultry in late 2003. It has infected 48 Indonesians so far and the country has the second highest total bird flu deaths in the world.
Infected fowl are the usual mode of transmission of the virus, now endemic in poultry in nearly all of Indonesia's 33 provinces.
Last week, workers culled around 1,600 chickens in Tasikmalaya region where the boy died.
Chickens at his home and around the village where he lived had died a few days before he fell ill. The boy's grandfather was a chicken farmer.
Separately, authorities have sent samples from a seven-year-old Indonesian girl who also died last 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 have not shown all of the traits that are known so far to allow it to spread easily among people.
Indonesia's government has been criticized by some experts for what is perceived as its lack of resolve in stamping out the H5N1 virus.
Unlike neighboring Thailand and Vietnam, which have conducted mass culls to get rid of sources of infection, Indonesia has only carried out selective culling and only in places where there are known outbreaks of H5N1.
The government has cited the huge expense involved in carrying out a mass cull in a sprawling country of 17,000 islands where there are millions of backyard fowl.