DNA tests confirmed the H5 strain of the virus at a farm in Miyazaki prefecture in the country's southwest after its owner reported yesterday that several chickens had suddenly died, the local government said.
Officials began the slaughter today and asked farms within a 10 kilometre radius not to move their poultry outside of that geographic area.
The case comes about two weeks after the government ordered the slaughter of some 4 thousand chickens at another poultry farm in Miyazaki- the first confirmed outbreak of bird flu at a Japanese poultry farm since April.
Officials also set up stations to disinfect vehicles travelling on major roads near the affected farm to prevent the virus from spreading.
It is uncertain whether there is a link between the first outbreak and the second, a farm ministry official said Monday, adding that further testing of the strain would be conducted at a government-backed research institute.
The second poultry farm is about 100 kilometres away from the site that was affected earlier this month.
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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