The report, commissioned by ministers to assess the potential effects of cultivating GM food in Britain, concludes that there are insufficient safeguards to stop the creation of hybrid multi-resistant plants.
It lists a series of "gaps" in the UK's regulatory framework, leaving Britain's wildlife at serious risk of damage from genetically modified plants and other intensive farming methods.
The news comes as the Health and Safety Executive, responsible for monitoring GM crop trials, has revealed that in the six months between April and October this year more than one in 10 of the 49 sites inspected during that period had been breaking the regulations governing trials. This week it is expected to prosecute Monsanto for such breaches - the first ever criminal case of its kind.
The study, written by civil servants after widespread consultation with government advisers, also warns that the commercial growth of GM crops could lead to more pesticides being sprayed on Britain's fields.
The study calls for the creation of a new watchdog body, composed of environmentalists, scientists and farmers, to oversee the effects of genetically modified plants. It suggests a new law may be necessary to make sure that farmers do not grow fields of genetically modified plants next to each other. This could lead to the creation of "Frankenstein" multi-resistant plants.
The report was commissioned earlier this year after an outcry by wildlife bodies and green groups about the lack of information on the long-term effects of GM crops.
It was trumpeted as a key aid in determining whether or not to go ahead with the commercial planting of GM crops in Britain.
But the document, which was supposed to have been published in September, has been held up within Whitehall, and government sources say that its original conclusions may never see the light of day.
Sources close to the Government say that ministers have delayed publishing the report because of its controversial implications, and that the first draft has been watered down.
English Nature, The Royal Society for the Protection of Birds and members of the Government's Advisory Committee on Releases to the Environment (ACRE), which advises the Secretary of State for the Environment on the effects of GM organisms on human health and environmental safety, were consulted during the drafting of the report. They have all been instructed not to discuss its contents.
Green groups want the Government to reveal the conclusions of the report immediately.
"Friends of the Earth is very insistent that this report be published in its full form," said Adrian Bebb, food and biotechnology campaigner. "If the Government's own civil servants are concerned about the implications of GM crops on wildlife we should be told what their conclusions are. Once GM crops are grown there is no going back."
There is now a voluntary moratorium on planting genetically modified crops in Britain although wider testing, involving the planting of fields of oilseed rape, will go ahead next year.
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