The farm in Mitoyo city reported that a total of 3,800 chickens had died between Sunday and Wednesday and a detailed examination confirmed that the virus was likely to be the highly pathogenic H5 strain, Japan NHK public broadcaster said in a news report.
Kagawa Governor Hamada Keizo said on Thursday that immediate measures will be taken to prevent the virus from spreading and has begun the process of culling roughly 330,000 chickens at the farm.
He has also planned to request the dispatch of Self-Defense Force personnel for assistance.
Prefectural officials have said that it will take about 10 days to cull and bury the chickens.
The prefecture is banning the transport of chickens and eggs within a 3 km radius of the farm.
Samples taken randomly from 2 million chickens at 26 poultry farms in the area will be tested for the virus.
According to authorities, this is the first cases of avian flu this year after the H5 strain was detected at a poultry farm in the same prefecture in 2018.
The development comes in the midst of the ongoing coronavirus pandemic.
Japan has so far reported more than 103,000 confirmed Covid-19 cases, while the death toll stood at 1,794.