Mr Yewdall said the Guernsey cows would be difficult to replace
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Nearly 50 cows in north Devon have been slaughtered after contracting the bovine tuberculosis disease.
Tony Yewdall, 69, who runs West Webbery Farm, near Bideford, Devon, said the loss was "devastating".
He wants tougher government action to tackle the disease, particularly in seeing if badgers spread it.
The Department for Environment, Food and Rural Affairs (Defra) said it was policy not to kill or take badgers away during a current culling trial.
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It is the worst possible time this could happen to us
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The 48 sick Guernsey cows, which are about a quarter of his pedigree milking herd, were collected from Mr Yewdall's family-run farm early on Wednesday morning.
Mr Yewdall said two adjoining farms also had cattle infected with the disease and warned of a possible "epidemic".
Mr Yewdall, who has owned the farm for 20 years, was told in February that the cows would have to be slaughtered.
He has around 350 animals in total, of which 200 are milking cows. As they are pedigrees, they will be difficult to replace, he said.
He said: "They are just about to calve so it is the worst possible time this could happen to us."
He said the government should consider issuing special licences to farmers in badly-hit areas to cull badgers, which many believe spread bovine TB.
He said: "We feel this is a dire situation where our livelihood is at stake. I have got a son and a grandson here.
"It could build up worse than foot-and-mouth. It is a terrible thing, and they are not doing anything about it."
Improving biosecurity
The farmer stressed that there is no risk to the public from bovine TB because all milk sold for human consumption was pasteurised.
A spokesman for Defra said it was policy not to issue licences to kill or take badgers to prevent the spread of bovine TB while the government's randomised badger culling trial is under way.
He added: "We have considered Mr Yewdall's particular circumstances carefully, but no reason can be identified for treating this breakdown differently from any other.
"There are measures that farmers can take to reduce the risk of disease transmission from badgers by improving herd biosecurity.
"Advice on these measures is available from Defra and an offer of a visit by a wildlife adviser was given to Mr Yewdall."