Richard Yates says farmers could be faced with "considerable losses" of animals over the outbreak.
The Ulster Farmers' Union rejects a claim that it is trying to dictate policy after a cattle cull.
The disease gives farmers another challenge while they are already dealing with extreme heat.
Farmer Kim Dart, from South Molton in Devon, says she dreads checking her flock each morning.
The Agriculture Minister Andrew Muir says he will continue to engage with the Ulster Farmers' Union.
The chief vet concedes the virus is "here to stay" as the UK experiences warmer summers.
The latest Defra figures show the south-west of England is the most impacted area across the UK.
Andrew Keys was among hundreds of farmers who protested outside an emergency Daera committee meeting on Monday.
The NFU recommends widespread vaccinations as a case of the virus is confirmed in East Yorkshire.
