The Commission authorised the ban, which also prohibits the use of around 700 non-GM maize varieties in Poland, after it was given unanimous approval by EU member states.
The move is the latest in the ongoing row over genetically modified (GM) crops and food, and threatens to put the EU back on a collision course with the World Trade Organisation.
Poland's government, which passed the ban in the country's parliament last week, used cultivation rules set out in a 2002 EU Directive to justify its stance.
The clause says any Member State can ban crop varieties that are not suitable for growing on its land. Poland said both the GM and non-GM maizes had a long growing cycle and, because of the country's climate, would not reach the necessary ripeness needed for harvesting.
The ban has caused considerable debate in Poland, which agreed to drop a previous ban on GM crops before joining the EU in May 2004.
Several leading Polish scientists led a public appeal against re-introducing a GM ban because it could hamper research. The US Foreign Agricultural Service also reported that the Polish Senate was split on the proposal.
The victory for those in favour, which can now only be dashed by Poland's president Lech Kaczynski, could lead to serious repercussions on the world stage.
The World Trade Organisation (WTO) ruled in February this year that the EU and six member states had broken free trade rules by imposing a moratorium on GM imports between June 1999 and August 2003.
The decision, in theory, opened up the EU market to GM food.
The issue, however, remains contentious and strong public opinion against GM food has forced major food companies and retailers to issue non-GM guarantees to customers in recent years.
Arguments over the safety of GM food have also been joined by debate on how GM and non-GM crops could co-exist, ensuring consumers continue to have a choice.
Anti-GM campaigners argue that GM crops will cause widespread contamination, leaving consumers with no GM-free choice at all. Pro-GM forces on the other hand argue that consumers must be given the choice, and that the WTO ruling backs this up.
The safety and co-existence debates have consistently split member states in the European Council over the last couple of years, despite the Commission approving several GM crop varieties for use in animal feed.
Cost may, in the end, be a crucial factor. Europe's opposition to GM food could increase costs for food firms by up to 16 per cent in some cases over the next three years as it becomes ever harder to source non-GM supplies, according to a report commissioned last year by Agricultural Biotechnology Europe.