The Environmental Audit Committee proposed the moratorium in a report on biofuels released on Monday, after concluding that biofuels were, "an expensive and ineffective" method of reducing carbon emissions.
EU energy commissioner Andris Piebalgs disagrees with the move, saying that any comparisons based on sustainability must first be made between biofuels and the continuing use of oil for fuel.
In a statement released in response to the report, the commissioner said: "The report fails to mention that until other technologies such as hydrogen become competitive, the only alternative to biofuels is oil.
"This means a shrinking source of energy with serious environmental concerns in the regions where it is produced, that generates large amounts of CO2 not only when it is burned, but also when is extracted, transported, and refined," he continued.
However EAC Chairman, Tim Yeo, claims that without proper regulation of the use of biofuels, its use cannot be sustainable.
He said: "Without this reassessment, biofuels could lead to a range of environmental impacts including water pollution and biodiversity loss.