Multiple chickens were found dead at the farm on Tuesday and genetic testing revealed the presence of the H5 strain of the avian influenza virus, Xinhua news agency reported.
In response, the Kagoshima Prefectural Government began culling approximately 120,000 chickens at the farm early on Wednesday.
The affected area includes 89 poultry farms within a 10-kilometre radius, housing approximately 5 million chickens.
This marks the 10th case of avian influenza at a poultry farm in Japan this season, according to the ministry.