Friends of the Earth says it has received documents that quote the Commission as saying that there are "large areas of uncertainty" and that "some issues have not yet been studied at all".
These documents were written by the Commission and submitted to the WTO. The WTO ruled last month that any European ban on GM imports contravened the rules of free trade.
The documents also suggest there have been disagreements between the Commission and the European Food Safety Authority (EFSA), the EU agency that is responsible for GM risk assessments.
In one example, FoE says that the Commission criticises the EFSA for not requiring further investigations after dismissing scientific evidence that showed that a certain GMO had negative effects on earthworms.
At the same time however, FoE points out that the Commission has pushed through the approval of seven GM foods over the past years. This was carried out despite a lack of support from the majority of member states.
"This is a political scandal," said Friends of the Earth GM campaigner Clare Oxborrow.
"The European Commission must call a halt to the sale and growth of all genetically modified food and crops given the serious concerns over their safety that have come to light.
"When the EU Commission broke the moratorium and forced GM foods into Europe, it told the public they were safe. But the Commission clearly knew this was not the case and was prepared to recognise the risk behind closed doors."
But Europe is nonetheless moving ahead with GM technology. The EC recently adopted an overview of the state of implementation of national co-existence measures, which led to this month's Vienna summit.
In addition, the biotech industry is adamant that stringent safety measures are in place to ensure that GM food presents no danger to humans.
Simon Barber, director of the plant biotechnology unit at EuropaBio - the European association for bioindustries, said that co-existence of GM and non-GM crops is already a reality in Spain.
"A quarter of a million hectares of Bt maize has been grown since 1998 with no substantiated problems," he said.
"This is also the situation in other parts of the world, where millions of hectares are grown without problems."
In addition, he claimed that FoE is purposefully mixing up the argument and frightening consumers. He said that the recent WTO ruling was concerned solely with trade issues.
"It was the industry's view that the regulatory process was not being properly implemented, and that some Member States were following illegal bans. Environmental protection has never come into this discussion. The only thing being challenged was the trade rules."
Nonetheless, Friends of the Earth has both called for an immediate suspension in the use and sale of all GM foods and crops until these safety issues have been addressed. The Commission's scientific arguments at the WTO can be downloaded from the FoE's site: http://www.foeeurope.org/biteback/EC_case.htm.