Ministers from the 28-nation bloc overcame a year-long deadlock to agree a reduction in the use of 'first generation' biofuels, which are made from crops such as corn, beetroot or rapeseed.
The new deal will cap the use of fuel made from food products to 7.0 per cent of transport sector energy use by 2020, down from an original target set in 2009 of 10 percent.
The EU has been a leader in driving the takeup of fuels made from crops -- so-called first-generation biofuels -- to replace fossil fuels like oil in a bit to cut global carbon emissions.
Critics also argue the conversion of land to grow biofuels, particularly in the peaty mangrove swamps of Southeast Asia, means they are not the environmental panacea the EU has touted them to be.
The European Commission, the EU's executive, originally backed a 5.0 per cent limit and acknowledged Friday's was weaker than hoped.
"But better this than no decision at all," EU Energy Commissioner Guenther Oettinger said.
Activists, however, said the deal would not be enough to limit the impact of biofuels on the world's increasingly tight food supply as the global population increases.
"In a starving world, phasing out the use of food for fuel is the only sensible thing to do," he said.
The measure now goes to the European Parliament, which is pushing for a 6.0 per cent limit.
Italian Energy Minister Claudio de Vicenti, whose country takes over the EU's rotating presidency next month, admitted its passage "will be difficult".
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