Robin Feakins' property, Sparum Farm in Kidderminster, Worcestershire, was chosen as a site to incinerate 5,000 cattle and 6,000 sheep which had been culled.
But Mr Feakins says the ashes from the carcasses were only buried six inches deep instead of the regulation three feet.
He also says that, without his knowledge, an unknown number of cattle which were burned or attempted to be burned were born before August 1996 and therefore potential carriers of the disease Bovine Spongiform Encephalopathy (BSE).
BSE concern
In 1988 concern was raised that BSE, the result of using recycling animal protein in animal feed, could be linked to the fatal brain condition Creutzfeldt-Jacob disease (CJD) in humans.
A ban on the use of meat and bone meal feed was brought in along with a slaughter policy for all affected cattle.
The link between BSE and CJD was firmly established and the European Union banned all exports of British beef.
The government also announced tighter BSE controls and a 30-month slaughter scheme was introduced in an effort to ensure that all cows over the age of 30 months at the time of slaughter did not enter the human food or animal feed chain.
Livelihood loss
In a written submission before the court, Mr Feakins says his land was left blighted and his livelihood threatened.
He has since abandoned his property and moved his family to a farm in Scotland over fears they could pick up BSE.
If successful, the action could force the government to treat the cremation site, which Mr Feakins estimates could cost more than £2m.
Mr Feakins is also seeking compensation for the loss of his livelihood.