The authorities began testing workers at the Jakarta zoo after dozens of birds there, including peacocks and eagles, tested positive for the often-fatal H5N1 form of the virus.
Bird flu has also killed four humans in the Indonesian capital, three in July, and a woman earlier this month. Three children are in a Jakarta hospital suffering flu-like symptoms.
Indonesia's Health Minister said two of the children are suspected to have contracted bird flu based on initial tests in Jakarta, while the third is under observation.
Indonesia sends blood from all suspected bird flu victims to Hong Kong for official results.
Georg Petersen, the World Health Organization representative in Indonesia, says the country is actively watching for the disease.
"I think what we see is heightened alertness, so possible cases are being investigated further," he said. "I think the fact that several cases have been popping up in a short time shows us that hospitals have been alerted."
Mr. Petersen says the virus is now endemic to Indonesia.
"What we have known since late 2003 there have been outbreaks in poultry and ducks across Indonesia... and we know it has come and gone in many places, so basically the H5N1 is established and circulated in domestic birds, and also probably wild birds in Indonesia," he said.
The H5N1 form of the bird flu virus first appeared in Hong Kong in late 1997, when it infected 18 people and killed six of them. It has since killed another 64 people in Indonesia, Vietnam, Thailand and Cambodia. In addition, tens of millions of birds have died or been culled across Asia, hurting the livelihoods of farmers.
The human victims have caught the disease from infected birds. But the World Health Organization warns that the virus could mutate into a form that spreads from one human to another, possibly setting off a deadly pandemic.
The WHO regional director for Western Pacific, Shigeru Omni, said at the opening of a WHO conference in New Caledonia that poor Asian farmers are a weak link in the fight to contain the disease. He said these farmers are reluctant to report bird flu outbreaks because of a lack of financial incentives to do so.
WHO says countries should hold a mass culling when an outbreak occurs, but some nations refuse. Indonesia has launched a vaccination drive for poultry, but has carried out only limited culling because it lacks the money to compensate farmers.