About 143,000 egg-laying chickens are being exterminated at the farm in Yokote city in Akita Prefecture, the ministry said in a statement on its website, adding that restricted zones up to 10 km (6.2 miles) from the site have been established.
Under the current situation in Japan, we do not believe that there is any possibility of avian influenza being transmitted to humans through the consumption of chicken meat or eggs," the ministry said.
But an increase in the number of people in China getting infected from bird flu this year is turning into a source of concern among epidemiological experts, especially as the world slowly recovers from the COVID-19 pandemic.
Outbreaks of bird flu have also been reported in recent days and weeks in Europe with farms in Poland the latest locations for infections, totalling 650,000 poultry.
Last winter, Japan had its worst season of winter flu on farms yet, with more than 3 million chickens culled and a quarter of the country's prefectures affected.
Japan has an egg-laying flock of around 185 million hens and a broiler population of 138 million, according to the ministry of agriculture.