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But the agency, which monitors pollution, was called in after gaps were seen in the walls of the former aircraft hangars at Barkston Heath, near Belton in Lincolnshire, and dead rats were found inside.
The Ministry of Agriculture, Fisheries and Food denied there was a major risk, saying only a tiny proportion of the cattle there would have been infected with BSE.
Agriculture Minister Nick Brown said: "I don't think there is a health risk, after all the rats are not available for human consumption.
"This is not product which is going to get anywhere near the human food chain."
To minimise the risk of mad cow disease getting into the human food chain, all cattle over the age of 30 months are cullled. Then, their carcasses are rendered and the remains burnt at very high temperatures to destroy the protein thought to cause BSE.
Locations revealed
But Britain has only one incinerator - in Southampton, Hampshire - capable of destroying the 80,000 tonnes of animals culled every year.
![[ image: width=150]](/olmedia/425000/images/_427153_hoof.jpg)
It can handle 15,000 tonnes of cattle a year, so 65,000 tonnes of meat and bonemeal need to be stored every year.
Mr Brown said: "We are trying to get planning permission for a second incincerator in order to speed up the incineration of this stuff.
"It is ironic that it is the Department of Environment, whose Environment Agency is looking at whether it is being kept securely, is also the department in control of planning consents."
The Observer reveals the location of the 13 secret dumps around the UK where the 400,000 tonnes of slaughtered cattle are stockpiled.
'Scared witless'
It quotes a group of councillors and environmental health officers who were invited by the Ministry of Agriculture to visit Barkston Heath.
District councillor David Lomas told the newspaper: "We went concerned and came away scared witless. We saw dead vermin and a dead pigeon in the stuff, showing quite clearly animals can get in and out.
"We saw gaps in the wall and ventilators spewing dust into the atmosphere."
'Weak' ministry rebuked over BSE
(18 Aug 99 | Sci/Tech)
UK Government joins beef war
(13 Jul 99 | The Economy)
Welsh farmers celebrate beef ban end
(09 Jul 99 | Special Report)
BSE: The long search for the facts
(22 Aug 99 | BSE Inquiry)
Britain's bill for mad cow crisis
(22 Aug 99 | BSE Inquiry)
Government braced for beef pressure
(02 Mar 99 | UK)
Ministry of Agriculture, Fisheries and Food
Environment Agency
BSE Inquiry
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