During an inspection at Pond Farm in Godalming last year, officials noticed the food Percy Podger was giving his cows looked unusual.
Tests by the government's Veterinary Laboratories Agency (VLA) showed it was pet food, intended for rabbits or guinea pigs and it contained mammalian meat and bonemeal (MMBM) which was probably bovine.
It is illegal to feed bovine material to cows because of the risk of humans contracting vCJD.
A Defra spokesperson said: "The basis for our actions is fully under-pinned by recent tests carried out by the VLA on Mr Podger's cattle feed. The test results showed that the pet food that Mr Podger was feeding his cows contained some bovine material and was unsuitable for use as cattle feed.
"As it is currently illegal to feed bovine material to cows destined for the food chain because of the risk of humans contracting vCJD, Mr Podger's 68 cows will have to be removed for slaughter by the State Veterinary Service, at the VLA."