Syamsul Bahri, director of Animal Health at the Agriculture Ministry, said on Friday the outbreak surfaced among backyard chickens in three areas largely spared from the 26 December tsunami that left 170,000 people dead or missing.
There had been no suspected human cases in Aceh, he said. Indonesia has recorded seven confirmed human deaths from the H5N1 avian virus since July.
"Up to now hundreds of chickens have died ... They are backyard chickens which had been bought from North Sumatra province," Bahri said, adding the outbreak was first detected three weeks ago.
Bahri said the outbreaks had not been detected in or near tented camps and barracks where hundreds of thousands of survivors of the tsunami disaster are still living.
Up to 200 chickens in the infected areas had been culled and hundreds more vaccinated to prevent the outbreak spreading.
"The most important thing is to handle the outbreak in the first stage and isolate the areas, then God willing we will not see transmission of the virus to humans," Bahri added.
Millions of chickens and other birds in Indonesia have died from the disease or been killed to prevent its spread since bird flu was first detected in fowl in the world's fourth most populous country in 2003. The virus has been detected among poultry in two thirds of Indonesia's 33 provinces.
Scientists fear the virus could mutate into a form which can pass easily among humans and trigger a global pandemic that could kill millions.