Health Minister Siti Fadilah Supari said on Wednesday that lab tests from Hong Kong showed the 38-year-old man and his two children, aged nine and one, had the deadly H5N1 strain of bird flu.
"It's confirmed. They died of the conventional bird flu virus which does not transmit from humans to humans," the minister said.
300 under observation
She added that it was not known when and where Iwan Siswara Rafei and his two daughters had been infected.
But she added that the authorities believed the three had contracted the disease at about the same time.
The family's house in Tangerang district, just southwest of Jakarta, is far from areas where there had been bird flu outbreaks, she said.
The virus may mutate to become
highly infectious, say experts
The man and his daughters died within days of each other in hospital in the first half of July after suffering from severe pneumonia.
About 300 people had been under observation for having contact with Rafei, including his wife, another daughter and the family's housemaid, and they had shown no signs of sickness, the minister said.
Agriculture Minister Anton Apriyanto has ordered a cull of poultry and pigs within a radius of three km from a known bird flu outbreak.
The ministry has confirmed the infection of bird flu in pigs in Banten province, raising concerns that the virus has taken a step closer to infecting humans in Indonesia.
The H5N1 strain of bird flu has so far been mainly transmitted between animals, but it has also killed more than 50 people in Southeast Asia since 2003.
Experts fear it could mutate into a highly infectious strain that can be easily transmitted from animals to humans or from humans to humans, unleashing a pandemic that could kill tens of millions of people.
Bird flu has swept through poultry populations in large swathes of Asia since 2003.
Tens of millions of chickens have either died or been slaughtered.
The disease has killed 38 people in Vietnam, 12 in Thailand, four in Cambodia, and - with the latest deaths - three in Indonesia.