The virus was detected in the analysis of duck fecal samples taken on November 18, according to the agency.
Japan's Ministry of the Environment has established a 10-kilometer (6-mile) monitoring zone in the region, where the virus was detected. It is yet unknown if the government is planning to test wild birds for the disease, according to Kyodo.
Experts do not rule out the possibility that the virus could have been brought into the region by migratory birds from South Korea, where a similar type of avian influenza outbreak was detected earlier this year. More than two million chickens and ducks were destroyed.
In November, outbreaks of avian influenza were reported in several provinces of China, as well as in the UK and the Netherlands.