The highly pathogenic H5 virus was detected through genetic testing of chickens at a farm in Kumamoto prefecture in the south, the ministry said on its Website.
A total of 1,100 chickens have died and about 112,000 would be culled, media said.
There is believed to be no risk of the virus spreading to humans through consumption of chicken eggs or meat, said Tomoyuki Takehisa, an Agricultural Ministry official.
It is the first bird flu case in Japan since 2011 when it was detected in Chiba prefecture, north of Tokyo.
© Thomson Reuters 2014