Umar Aup was admitted to a hospital in West Java province last Wednesday and left the next day on the orders of his family, who said they could treat him at home with a mixture of prayers and traditional remedies, said Dr. Eka Sony, a Health Ministry official investigating the case.
The 17-year-old remains very ill, said Sony, who visited him Sunday in his remote village, the AP reports.
Villagers said Aup and his cousin collected the carcasses of around 100 chickens that died suddenly last week and fed them to dogs, said Sony.
Sony said Aup's cousin died after showing symptoms of the virus.
Health officials have said they suspect that many Indonesians have died from bird flu unreported because they no tests were performed.
Laboratory tests have confirmed Aup has the virus.
Just under 60 percent of those who contract the virus die from it, according to a breakdown of cases reported to the World Health Organization.
The case shows the challenges facing health workers dealing with bird flu in Indonesia, a sprawling country which last week became the country worst hit by the virus. It has recorded 44 deaths.
The H5N1 virus has killed at least 138 people worldwide since it began ravaging Asian poultry stocks in late 2003, according to a tally kept by the WHO.
The virus is rampant among Indonesia's billions of backyard chickens.