EU Commission plans, to hand individual member states the power to decide whether to grow or ban GM crops, would set a dangerous precedent, industry leaders have warned.
EU health commissioner John Dalli said governments needed more freedom and flexibility to organise the cultivation of GM crops next to unaltered or organic crops.
Mr Dalli said the EU should step in only if GM crops posed a health or environmental danger.
But the NFU said such a move would set a dangerous precedent for the European regulatory system and threatened both the internal market and farmer choice.
Under the proposals, member states will be able to decide whether to ban the growing of GM crops for "socio-economic" or "cultural reasons" with no regard to health or environmental safety, said an NFU spokesman.
"With this package, the commission has essentially absolved itself of any responsibility on a highly sensitive issue.
"We are very concerned that, instead of making decisions based on science, member states would be able to legitimately use coexistence measures to restrict GM plantings and to lower labelling thresholds at either national or regional levels," the spokesman said.
This has the potential to severely disrupt internal markets and cause uncertainty throughout the agriculture and food supply chains, as well as adding further confusion for consumers.
"It may also lead to severe political and legal pressure on national governments and compromise their ability to make science-based policy decisions about GM crops," he added.
NFU Scotland president Jim McLaren said that leaving GM cultivation policy to member states and regions, would create the potential for GM policy to change with every election.
"GM policy across borders, such as Scotland, England, Wales and Northern Ireland, could be very different.