Officials and residents in Asahan district of North Sumatra province said villagers began showing symptoms of avian flu after a large number of chickens died suddenly last week.
The nurse at Asahan district's Kisaran hospital said three people had died after suffering bird flu-like symptoms in Air Batu village.
"According to residents there, a number of chickens died suddenly last week followed by several pigeons. Days later, three people died with the same ailments," the nurse, Mariana, told AFP.
Another 13 people had been admitted to the hospital with "high temperatures and respiratory problems," she said.
Two of these -- a baby boy and a seven-year-old girl -- were transferred early Wednesday to a bird flu isolation unit at Adam Malik hospital in the provincial capital of Medan, officials said.
Adam Malik hospital spokesman Sinar Ginting confirmed that blood samples from the two children were sent Wednesday to a health ministry laboratory in Jakarta for analysis.
"We are now waiting for the result," he said.
The father of the baby boy, Slamet Riadi, said a lot of poultry had died in the village a week ago. His baby developed a high fever and respiratory problems shortly afterward.
A spokeswoman for the health ministry could not be reached for comment.
The ministry, which has stopped giving regular bird flu updates, announced earlier this week that the human toll from avian influenza in Indonesia had risen to 112 with the recent death of a 19-year-old man.
The man was from a town adjoining the capital Jakarta on Java island.
Indonesia is the country worst-hit by the deadly H5N1 strain of bird flu, which can be passed from bird to human.
Experts fear it could mutate into a form easily transmissible between humans and kill millions in a global pandemic.