A group of vets from UK's Ministry of Agriculture (Maff) claim that the slaughter policy designed to eradicate foot-and-mouth disease has led to animals being culled without "rhyme or reason".
Channel 4News reported that a letter, signed by 40 vets, says that the scientists trying to combat the epidemic lack veterinary experience.
Vet Roger Windsor sent the letter to Tony Blair in which he said the fate of healthy animals should be decided by vets.
Maff says the Government's chief veterinary officer, Jim Scudamore, supports the Government's foot-and-mouth strategy.
In the letter, Professor David King, the British government's chief scientific adviser, and Roy Anderson, of Imperial College, were criticised for their lack of veterinary expertise.
Mr Windsor later commented: "The method that has been put forward by Roy Anderson means the disease will be eliminated by June 6.
"If we don't follow this model the slaughter might go on until July but we might end up slaughtering considerably fewer animals."
The letter to the Prime Minister stated: "Animals are being slaughtered without rhyme or reason, often weeks after the supposed danger farm has been eliminated.
"This scotched earth policy will undoubtedly result in the eradication of foot-and-mouth disease but it may be a pyrrhic victory. If we (vets) are not to be used as professionals, we must question why we are employed at all."
A Maff spokeswoman commented: "Our reaction to this is that the minister acts from the advice of the chief veterinary officer as well as the chief scientific officer."
PA