Japan has mobilised its military to help with a second mass cull of 230,000 chickens amid a spreading outbreak of a highly contagious strain of avian flu, officials said.

The highly virulent H5 strain was found in chickens at a farm in Joetsu city in Niigata prefecture, the local government said in a statement late Wednesday.

It said that 2,100 people, including 1,020 members of the military, were being mobilised in the effort to kill the chickens and contain the virus.

The chicken slaughter began late Wednesday and was expected to continue until Sunday, the statement said.

Authorities have also banned the transport of poultry and poultry products in areas close to the affected farm, while sterilising main roads leading to them.

The case comes after a cull of nearly 320,000 chickens began at another farm in Niigata and some 16,500 ducks were also to be culled at a farm in the northern prefecture of Aomori.

Farm minister Yuji Yamamoto urged Niigata prefecture to "enhance measures" to prevent the virus from spreading, according to Jiji Press.

Before the current outbreak, Japan's last confirmed case of avian flu at a farm was in January 2015.