Prior to the vote the EU had a "zero tolerance" policy on unauthorized GM crops, and shipments found to contain any trace of GM that was not yet approved in Europe were turned back at the port, Britain's Daily Telegraph reported Tuesday.
However, in a significant victory for the GM lobby, EU member states have voted to allow imports containing up to 0.1 percent of unauthorized seed.
Last year Europe imported 33 million tons of soy, mostly approved GM varieties for animal feed.
Critics say if the European Parliament and Council approve the vote those shipments could contain GM seeds that are authorized in a "third country" but may not even have been tested in Europe.
Some of the unauthorized seeds have been bred for certain traits for industry that may be inappropriate in the food chain, they say.
"We think it is a major concern because it is a foot in the door to allow unauthorized products into the food chain," Helen Wallace of the group Genewatch said. "That could include crops modified to produce industrial chemicals or pharmaceuticals or for biofuels."