The campaigners claim that the Government's six-week public consultation on GM, which ended this month, was "severely flawed".
Peter Riley, campaigner at Friends of the Earth, said: "Far from giving GM crops the green light, this report admits that there are gaps in our scientific knowledge and significant uncertainties about the long-term impact of GM food and crops on our health and environment."
The Soil Association, which certifies foods as GM-free, said the findings left major areas in the debate without investigation.
Director Patrick Holden said: "BSE should have taught us that the absence of evidence of harm is not evidence of safety, particularly when no long-term feeding trials have been done."
Friends of the Earth said the debate was underfunded and lacked clarity in its objectives and together with Greenpeace is calling for it to be extended. Greenpeace has linked up with the Consumers' Association and chemical giant Unilever to launch an eight-week citizens' jury on GM, which it says will present an unbiased contribution to the Government's GM policy. Although the organisations are funding the inquiry, they will make no contribution to it.
"The public has been subjected to a barrage of propaganda courtesy of GM advocates as well as sceptics," said Charlie Kronick, chief policy advisor at Greenpeace. "Now a diverse group of people have the chance to take part in a proper discussion and reach their own conclusions."
Dr Mark Avery, director of conservation at the RSPB, said: "This report shows that eminent scientists, as well as environmental organisations, fear GM cultivation will adversely affect wildlife."