The outbreak was identified after multiple ducks were found dead on Sunday and genetic testing confirmed the presence of the virus by Monday morning, Xinhua news agency reported.
In response, some 2,500 ducks at the farm were culled to prevent the spread of the virus.
Authorities have established a 3-kilometre movement restriction zone around the farm, limiting the transport of birds and eggs, and a 10-kilometre shipping restriction zone to prevent distribution outside the area.
This marks the 11th case of avian influenza at a poultry farm in Japan this season.