Workers on Sunday started culling 56,000 chickens kept at a poultry farm in Kumamoto, southwestern Japan, where DNA tests confirmed the H5 strain of the virus after owners reported sudden deaths in the flock on Saturday, a Kumamoto prefectural government official said.
Another 56,000 birds were slaughtered at a separate farm run by the same owner after it was identified as a location of possible infections, the official said.
"We finished the slaughtering operation late Monday and are now preventing the virus from spreading to other areas," the official said, adding that no further infections had been reported by Tuesday morning.
It was the first confirmed outbreak of bird flu in Japan in three years. Scientists say there have been no cases of the disease being contracted by people who have eaten poultry or eggs.
In Tokyo, agriculture, forestry and fisheries minister Yoshimasa Hayashi was also quoted by Jiji Press as saying: "We will do our best to contain (the outbreak) as quickly as possible."
The ministry has been warning farmers about infection risks, citing the continued spread of the disease in Asia, including in neighbouring South Korea.
Local authorities on Saturday banned movement of chickens from the two affected farms as well as other farms in their vicinities.
Authorities were sanitising areas around the two farms and testing birds at other area farms.
Officials were also setting up areas to disinfect vehicles travelling on major roads around the affected farms to prevent the virus from spreading further.