Commission spokesman Johannes Laitenberger put the new delay down to divisions within the European Union's executive arm, pitting environmentalists against the biotech industry.
"There were doubts and it was decided to seek more clarification," he said. "If the scientific evidence confirm that the product is safe, then it will be allowed."
Laitenberger said the European Food Safety Authority, which has never rejected a GM product, had been ordered to carry out more scientific analysis of the products.
EU member states hold responsibility for jointly deciding whether GM products should be allowed on the market but frequently are unable to make a decision because they are divided on the subject.
As a result, the decision reverts to the European Commission, which usually follows the advice of EFSA, which itself has so far always given favourable opinions towards GM products.
The GM products with pending applications for authorisation are potato strain made by German group BASF to be resistant to antibiotics and several strains of pesticide resistant maize strains.
The European Commission, which has not authorised a GM crop in the EU since 1998, faces growing pressure to resolve the matter.
The delay comes amid a growing storm over how Europe decides whether to allow GM products or not. Environmentalists and some governments, such as Germany and France, say that the current procedure ultimately leaves the decision with EFSA.
With EU governments deeply divided over GM technology, environmental groups seized on the move as proof that the European Union's complicated procedures for assessing such products was in shambles
Greenpeace GM campaigner Marco Contiero said: "Today's decisions are a huge vote of no confidence in the EU food authority and vindicate Environment Commissioner Stavros Dimas' concerns about scientific inconsistencies in the EU GMO assessment."
Although GM products are common in other parts of the world, they remain fiercely debated in Europe where a recent EU survey found that about 58 percent of European citizens are apprehensive about their use and only 21 were in favour.
Separately, the commission called on Austria to lift import bans on two GM maize strains which Vienna has kept in place even though the EU has lost an WTO a challenge against them.
© 2008 AFP
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