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There is not believed to be a threat to humans and a probe at the farm in Aberdeenshire has now been launched.
This is the first case of the disease in three years in the UK and the first confirmed in Scotland since 2008, it is understood.
The last outbreak in Britain was in Wales in 2015 when the disease was discovered on a dead cow.
The UK death toll from BSE (bovine spongiform encephalopathy) is currently at 177 since Stephen Churchill, 19, died of a fatal brain condition linked to mad cow disease in 1995.
Restrictions are in place at the farm in Scotland as an investigation into the outbreak continues.
A Scottish Government statement said: “This is standard procedure for a confirmed case of classical BSE, which does not represent a threat to human health.”
Chief Veterinary Officer Sheila Voas said: “I would urge any farmer who has concerns to seek veterinary advice.”
Panic gripped the UK in 1995 as more than four million cattle were slaughtered to stop the infection spreading.
More than 180,000 cattle were thought to have been struck down by the disease and the EU put a ban on importing British beef between 1996 and 2006.
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