A total of 23 birds were found dead at a poultry farm in the town of Shintomicho in southwestern Miyazaki prefecture, the ministry said in a statement Tuesday.
"Seven samples out of 13 were positive in an initial examination checking whether there is a contamination by the bird flu virus," an official of the Miyazaki prefectural government told AFP.
They will cultivate the virus and send it to an animal laboratory to determine whether it is the toxic type of avian influenza.
The poultry farm in the suspected case owns some 93,000 chickens providing eggs for human consumption.
If confirmed, it would be the fourth outbreak of bird flu across Japan this month, amid fears that avian influenza could spread further.
Two cases of the virulent H5N1 strain were detected earlier this month in Miyazaki prefecture, while a third case of bird flu whose strain has yet to be verified was confirmed Monday in western Okayama prefecture.
H5N1 has killed around 160 people across the world since late 2003 and can be transmitted through contact with infected birds' waste.
Health officials have warned that if the disease mutated into a form easily transmissible by humans, it could cause a pandemic with the potential to kill millions of people.
Japan confirmed an outbreak of the H5N1 strain of bird flu in January 2004. Since then, the nation has seen several further outbreaks of the H5N1 strain as well as the less serious H5N2 virus.
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