DNA tests confirmed the H5 strain of the virus at a farm in Miyazaki after its owner reported more than 20 sudden deaths among his poultry on Sunday and yesterday, the agriculture ministry said.
"We confirmed at least three of the chickens tested positive for the virus," a ministry official said. "The Miyazaki government has already started culling all the chickens at the farm."
It was the first confirmed outbreak of bird flu at a Japanese poultry farm since April. Some wild birds that were found dead in southwestern Japan tested positive last month.
Officials were also setting up stations to disinfect vehicles travelling on major roads around the affected farm to prevent the virus from spreading further.
Prime Minister Shinzo Abe ordered the farm ministry to "promptly take thorough measures for epidemic prevention," a statement said.
Japan's agriculture ministry regularly warns farmers about the risk of infection, citing the continued spread of the disease in Asia, including in neighbouring South Korea.
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