The Soil Association said that businesses with turnover of £950m were "left in the cold" by the government consultation, which examined the coexistence between GM crops, non-GM crops and organic crops in England.
A delegation representing 74 organic businesses met at the House of Commons to express their concerns this week.
The meeting, hosted by Peter Ainsworth MP, shadow secretary of state for the environment, and Jim Paice MP, shadow agriculture minister, was organised by the Food and Drink Federation's Organic Group and The Soil Association.
"There is overwhelming evidence that one of the main reasons that consumers buy organic is to avoid eating food containing any GM," said Alex Smith of Alara, chair of the Food and Drink Federation (FDF)'s Organic Group.
"If the proposals set out by the government were implemented, very significant new economic burdens could be placed on organic food producers, manufacturers and retailers. Organic businesses will face enhanced risks of GM contamination, product recall and loss of their most valuable asset, the consumer trust that underlies their brand value".
The Soil Association also claimed that while the government met with a number of GM companies, during the consultation, no organic business was consulted directly.
"People who eat organic food will end up paying for a GM policy designed to benefit the GM companies," said Peter Melchett, Soil Association policy director.
"The government is putting at risk one of the fastest growing areas of the UK economy. Tesco's organic sales grew by 39 per cent last year. Organic farm shops and box schemes are seeing similar rates of growth."
Indeed, AC Nielsen Data also shows sales for Sainsburys' organic range has increased 18.4 per cent year on year. And the European organic market, worth €20.7 billion in 2004, has been growing by 26 per cent since 2001.
However the biotech sector, along with regulators, argue that adequate controls have been put in place to ensure that cross-contamination is not an issue.
Simon Barber, director of the plant biotechnology unit at EuropaBio - the European association for bioindustries said recently that thousands of European farmers grew GM last year, successfully co-existing with their neighbours.
In addition, Mariann Fischer Boel, member of the European Commission responsible for agriculture and rural development, pointed out that the question of how to cultivate a given GM crop alongside non-GM crops only arises if that crop has already been cleared as harmless by the EU's assessment system. That system she said, was arguably the strictest in the world.
Nonetheless, Melchett said that "warmly welcomed" the motion tabled in the House of Commons, which states that "consumers have the right to choose non-GM foods and that all foods containing GM material, or that come from livestock fed on GM, should be clearly labelled as such", and that 0.1 per cent GM "should be the trigger point for GM labelling".
"We hope it is not too late for the Government to change their pro-GM stance, which threatens public trust in organic farming and food," he said.