Agriculture Minister Ilse Aigner said U.S. seed maker Monsanto's MON810 genetically engineered corn product "presents a danger for the environment."
Genetically modified organisms, or GMOs, are common in the U.S. but controversial in Europe, where activists have protested their use and torn up GMO crops.
In 2004, the European Union authorized the planting of MON810 seeds, which produce a toxin to ward off insects. Monsanto claims this genetic trait precludes the need for dangerous pesticides, but opponents fear the seeds will spread and alter the natural surroundings.
France, Greece, Austria and Hungary have also imposed "safeguard" bans on the MON810 variety, citing studies that find it unsafe to the environment.
In March, EU environment ministers defeated a European Commission proposal that would have forced Austria and Hungary to lift their bans. Germany will join France and Greece in facing scrutiny from the Commission for their bans.
Aigner, a member of the Christian Social Union, the Bavarian sister party of Chancellor Angela Merkel's Christian Democratic Union, had been criticized for caving in to pressure from her heavily agricultural constituency to support the ban.
"Contrary to some assertions, my decision is not a political one," Aigner said.
Environmental groups hailed the decision.
Hubert Weiger, president of the German branch of Friends of the Earth, praised Aigner for "not buckling under pressure from a large biotech company."