Cattle and sheep at the farm within the protection zone set up around last Wednesday's outbreak near Egham, Surrey, had already been slaughtered on suspicion of the virus and when the animals were examined at slaughter, foot and mouth disease lesions were found, Defra said.
The case is the third since the virus resurfaced in Surrey last Wednesday and the fifth since the original outbreak at a farm in Normandy, Surrey, last month.
A site in Wales is also under investigation after it was linked to the latest case in Surrey, according to reports in The Times.
Meanwhile, animals will not be vaccinated against the disease at this stage, Defra has said.
“It has been decided not to vaccinate at this time because the risk of spread of disease outside of the Surrey area is still considered to be low at the present time,” said chief veterinary officer Debby Reynolds.