The boy from Cilegon in Banten province, just west of the capital Jakarta, was Indonesia's 81st bird flu victim. Contact with infected birds is the most common form of transmission of the deadly virus to humans, experts say.
Memed Zulkarnaen, director of the agriculture ministry's bird flu unit, said no infected poultry had been found within a radius of up to 300 metres (yards) from the boy's home.
"The Indonesian medical community is still puzzled and does not understand from which source the victim was infected with the bird flu virus," he told AFP.
"We are puzzled because the H5N1 virus needs to 'stick' to an object such as poultry and cannot freely circulate in the air," he said.
Asked whether there was a possibility the boy had contracted the virus from another person, Zulkarnaen said it was too premature to tell and investigations involving personnel from the UN's health and agriculture agencies were ongoing.
Sardikin Giriputro, deputy director of Jakarta's Sulianti Saroso hospital, where the boy died, told AFP on Tuesday that the boy had visited relatives who lived near a zoo elsewhere in Banten province, four days before he fell sick.
Indonesia is the nation worst hit by avian influenza. It confirmed its first human case in July 2005, but the source of infection in that particular case was never determined.
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.
Separately on Wednesday, the national committee overseeing Indonesia's bird flu fight along with UNICEF were to begin distributing 7,000 protective kits to villages in Banten province, where at least 10 bird flu deaths have occurred.
The kits contain gloves, masks, soap, an informational VCD, a banner and booklet. About 100,000 kits were distributed in high-risk areas in May, a statement from the committee said.
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.