He added that two other Indonesians in their 30s, who also tested positive for the H5N1 virus, were being treated in the capital.
Suyono said there were no obvious explanations for the sudden surge of cases.
"We need to carry more tests and investigation first to be really sure," he told reporters.
It is not clear how the deceased boy, who was treated in different hospitals for two weeks, had contracted the disease.
The woman is thought to have contracted the disease from fowl kept at a poultry slaughterhouse near her home.
Contact with sick fowl is the most common way of being infected by the virus which is endemic in bird populations in most parts of Indonesia where humans and poultry live in close proximity.
Although bird flu remains an animal disease, experts fear the virus could mutate into a form easily passed from human to human and spark a global epidemic.