The organisation claims that nearly all of the pork, milk and dairy products in UK supermarkets are produced from animals fed on GM crops and that consumers are being deceived because this is not shown clearly on labels.
Although the major UK supermarkets removed all of their own-label food made directly with GM ingredients by October 2002 in response to customer concerns, most multiples do not prohibit the use of GM animal feed.
There is no requirement to label food produced from GM-fed animals and food industry marks such as the 'Little Red Tractor' and 'Freedom Foods' do allow animals to be fed on GM crops.
The Soil Association says that this has allowed a "GM stealth invasion of the UK food chain," which is denying customers their right to make fully informed choices. It insists that the only food standard that guarantees the non-use of GM feed is organic.
Patrick Holden, Soil Association director said: "This amounts to deception on a large-scale. This is not just accidental contamination, hundreds of thousands of tonnes of GM grain are being used to produce our food each year.
"Biotechnology companies have clearly used imported animal feed as a Trojan Horse to introduce GM into the UK food chain, despite the fact that the British public have voted overwhelmingly against GM.
"The research on the presence of GM DNA in food from GM-fed animals and the impacts on animals is alarming.
"We urge the public to only buy meat and dairy that are known to be produced from non-GM fed animals, and to write to the supermarkets and ask them to stop allowing the use of GM feed.
"While it is excellent that Marks & Spencer and the poultry industry have restricted GM feed already, all retailers and food sectors should follow their lead.
"We also call on the supermarkets to label these products so they are being honest with their customers."
The Soil Association is trying to raise consumer awareness of the GM issue over concern that future supplies of non-GM feed will be threatened unless there is pressure on the food industry to ensure that meat and dairy products come from livestock raised on non-GM feed.