It is the second to be confirmed this week, after another strain of avian influenza was identified at a commercial premise in Kent.
All 13,500 birds on the Cheshire farm near Frodsham will be humanely culled to stop bird flu from spreading following the outbreak, the government said.
The outbreak was confirmed at the commercial broiler breeder rearing farm on Monday, according to the Department for Environment, Food and Rural Affairs (Defra).
On the same day, there was an unrelated bird flu outbreak confirmed at a farm near the town of Deal in Kent, which involved a different strain of the virus.
The H5N8 strain of bird flu has been detected at the Cheshire farm – which Defra described as a “highly pathogenic strain related to the virus currently circulating in Europe”.
It comes weeks after the UK raised its bird flu threat level from “low” to “medium” after two swans in the Netherlands were infected with the same strain of avian influenza.
The risk to public health from the virus is very low according to Public Health England (PHE), with Dr Gavin Dabrera, a PHE consultant in acute respiratory infections, saying there have never been any confirmed cases of H5N8 in humans.
The Food Standards Agency says that the avian influenzas pose a very low food safety risk for UK consumers.
Referring to the Cheshire outbreak, Christine Middlemiss, the UK’s chief veterinary officer, said: "Immediate steps have been taken to limit the risk of the disease spreading and all remaining poultry at the farm will be culled.
"Birdkeepers should remain alert for any signs of disease, report suspected disease immediately and ensure they are maintaining good biosecurity on their premises.
"We are urgently looking for any evidence of disease-spread associated with this farm to control and eliminate it."
Wild birds migrating from mainland Europe during the winter period can spread the disease to poultry and other captive birds, the government said, as it announced a "detailed investigation" to determine the most likely source of the outbreak.
Additional reporting by Press Association
Join our new commenting forum
Join thought-provoking conversations, follow other Independent readers and see their replies