Slaughter of some 42,000 chickens was ordered by Japan on Monday, after officials confirmed the country's second bird flu outbreak in less than a month.
DNA tests confirmed the H5 strain of the virus at a farm in Miyazaki prefecture in the country's southwest after its owner reported Sunday that several chickens had suddenly died, the local government said.
Officials began the slaughter Monday and asked farms within a 10 kilometre (62 miles) radius not to move their poultry outside of that geographic area.
Local authorities locked down that farm and others nearby, with the movement of chickens banned while the area was being sanitized.
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.