The World Health Organization has confirmed that a 23-year-old male poultry worker currently undergoing treatment in Sumatra has bird flu.
The case is Indonesia's 33rd case of the virus in humans.
Indonesian health officials say the man is being treated at the M Djamil hospital in Padang, in West Sumatra.
He had apparently been working at a chicken farm in West Java before he became sick.
Indonesia has had 23 confirmed deaths from avian influenza since 2003, but despite having the second highest death toll of any country, U.N. bird flu coordinator David Nabarro is not recommending a mass culling of fowl in Indonesia.
Nabarro, who is in Jakarta as part of a five-nation Asian visit, said the industry was too important for the local economy.
The Indonesian government has resisted the mass culling conducted in other countries because it is an expensive and impractical policy in a country where keeping a few chickens or ducks in the backyards of homes is common practice.
Indonesia has had the highest human bird flu deaths of any country so far this year, killing at least 12 people and as elsewhere the cases have all stemmed from contact with birds that were infected.
The highly pathogenic strain has affected birds in about two-thirds of the country's provinces and eradicating the virus is an impossible, task in the archipelago of 17,000 islands and 220 million people.
Nabarro has acknowledged government progress in dealing with the bird flu issue, and has called for more to be done to raise public awareness of the disease.