Indonesia has seen its toll from the deadly H5N1 virus grow steadily since 2005 when the first confirmed human deaths occurred here.
"A boy who died on July 8 has been confirmed by two tests as being positively infected," Ningrum, from the ministry's National Bird Flu Information Centre, told AFP.
"The toll is now at 102 infected, and 81 dead."
The primary school student was from the industrial town of Cilegon, 72 kilometres (50 miles) west of the capital Jakarta.
The boy, identified only by the initials FZ, died at Jakarta's Sulianti Saroso hospital, Indonesia's main centre for treating victims of the virus.
He showed symptoms on July 1 but was only admitted to hospital four days later and immediately transferred to Jakarta.
Ningrum said it was unclear whether the victim had come into contact with dead or infected poultry. Contact with infected birds is the most common form of transmission of the deadly virus to humans, experts say.
The UN health agency said last month that though the fight against bird flu had improved around the world, the situation remained critical both in Indonesia and Egypt. The frequent contact many people have with domesticated birds elevates the risk of transmission and mutation.
In Indonesia alone, the World Health Organisation estimates that there are more than 13,000 poultry markets, where birds from many different places are exposed to each other.
Scientists worry the bird flu virus could mutate into a form easily spread among humans, leading to a global pandemic with the potential to kill millions.
The fear stems from past influenza pandemics. A flu pandemic in 1918, just after the end of World War I, killed 20 million people worldwide.
Indonesia stepped up its campaign this year to battle bird flu, barring Jakarta residents from the popular practice of keeping poultry in their backyards.
Officials were criticised for being slow to act when avian influenza first appeared in the archipelago nation.
Since 2003 the H5N1 virus has infected 317 people, 191 of whom have died, according to WHO figures published before the latest death. Some 250 million poultry have also been culled, or have died from bird flu.