The European Parliament environment committee said member states should be allowed to disregard the EU's current authorisation procedure, where the European Food Safety Authority (EFSA) makes the decision on GM safety, and make their own scientific assessment.
Under their proposal, countries would be able to use environmental grounds, such as pesticide resistance or invasiveness of crops, to bring in national bans, even if the EFSA had already deemed concerns unfounded.
Dr Helen Ferrier, the NFU's chief scientific adviser, said the MEPs were ignoring sound science and jeopardising food security.
"The European GM authorisation procedure is already the strictest and most highly scrutinised in the world. So the idea that member states would need to do their own scientific assessment seems to be more for political reasons," she contended.
"We urge MEPs to have a sensible GM debate in Europe based on sound science. We have a huge global challenge to feed a population that is due to hit nine billion by 2050 while having less impact on the environment and tackling climate change," she added.
"To achieve this we will need every weapon in our armoury. That includes GM crops that have been adapted to cope in dry conditions, need fewer pesticides and offer nutritional benefits."