Local authorities say this is the first such outbreak in the past 11 years.
On Sunday, workers at a farm in Aichi discovered an unusually high number of dead chickens. Out of 13 dead chickens, six were found to have suffered from bird flu.
According to media, another 34,000 chickens were culled in the prefecture of Kagoshima amid a bird flu outbreak.
Over the past weeks, Japan has registered bird flu outbreaks in the prefectures of Okayama, Kagawa, Miyagi, Aomori, Wakayama, Tottori, Kagoshima as well as on the island of Hokkaido. In total, about 3.3 million chickens have been culled in the country since the season's first outbreak on October 28.