The Soil Association is a lobbying and certification organisation for organic food and farming.
The report could instil further fears in a public already skittish about the safety of GM foods due to the apparent lack of long-term scientific studies into the health risk of modified crops.
If pressure is brought on supermarkets to enforce an anti-GM policy, the study could eventually lead to processors having to track and trace the source of their meat supplies.
The organisation also claims that new scientific evidence, reviewed in the report, shows that small amounts of GM DNA end up in milk and animal tissues of GM-fed animals, contrary to the assurances from the FSA.
"In addition, at least 13 animal feeding trials now show a range of alarming health effects in animals fed GM -- lesions in the gut, toxic effects in body organs, unexplained deaths and stunted growth in their offspring," the Soil Association claimed.
The Soil Association said its study found around 60 per cent of the maize and 30 per cent of the soya used as feed by dairy and pig farmers is made up of GM crops.
"This means that most of the non-organic milk, dairy products and pork being sold in the UK is from GM-fed animals," the Soil Association concludes.
The organisation noted that all supermarkets are widely allowing the use of GM feed in their meat supplies, except for their fresh own-label chicken, turkey and eggs.
"Due to a loophole in the law, none of this food is labelled as 'GM' so it is difficult to avoid," the Soil Association stated.
M&S was commended for being "ahead" of the competition as as all milk and fresh meat from the chain is sourced from non-GM fed animals.
However M&S does not not require non-GM fed animals for their frozen and processed products.
At the moment, 'organic' is the only food type which prohibits GM feed, the Soil Association stated.
The Soil Assocation called for public action to stop the use of GM in animal feed, including bring pressure to bear on supermarkets, food processors and restaurants.
The Soil Association report is available here: http://www.soilassociation.org/gm