The environmental group staged a protest at EU headquarters, arguing the crops pose a major risk to insects like butterflies and could damage local ecosystems.
Under heavy pressure from both industry and environmental groups, the EU's executive office is deliberating on whether to approve license applications for two biotech seeds for cultivation.
The products are the Bt-11 corn seed made by Switzerland's Syngenta AG and the corn 1507 product made by the U.S.-based Pioneer Hi-Bred and Dow Agrosciences.
Both varieties offer resistance to insects, including corn borers and certain butterfly species, and were deemed safe by the EU's food safety authority in 2005.
On Wednesday, Greenpeace activists called on EU executives to back EU Environment Commissioner Stavros Dimas' preliminary conclusions not to approve the two products for use in the 27-nation bloc.
Opponents of the two products fear they could threaten population levels of much cherished butterflies, like the Monarch species, as well as other insects.
"The proposal of Mr. Dimas is based on hard science," argued Marco Contiero from Greenpeace. He said Bt variety corn crops "are harming the environment, having unexpected and unpredictable effects."
Meanwhile, the European Federation of Biotechnology, a group of scientists and companies promoting the use of biotech crops, sent a letter to Dimas backing the products.
"GMOs are absolutely needed, there is no danger for health. No danger to the environment has been demonstrated," said Marc Van Montagu, who heads the group.
He rejected claims that the two GM seeds threaten insects other than those that try to feed off the crops during cultivation.
"There are no studies where scientists agree ... that butterflies die," Montagu said.
EU spokesman Johannes Laitenberger told reporters the approval was still under consideration by the European Commission's executive, which remains deeply divided on the issue. Unanimous backing is needed to approve the licenses.
The issue poses a headache for the Commission, which is trying to force reluctant EU governments to drop some national GM crop bans, amid increasing global pressure by Europe's trade partners.
The World Trade Organization has backed claims by the United States, Canada and others that a previous de facto moratorium on the use of GMO products in Europe is an unfair trade barrier.
EU Agriculture Commissioner Mariann Fischer Boel warned European farm ministers this week that continuing biotech bans could risk future supplies of cereals to farmers, threatening the supply of animal feed for Europe's pork, beef and chicken sectors.