This study attempts to evaluate the energy and environmental efficiency of the primary sectors of the EU member state countries. The evaluation is based on a non-radial Data Envelopment Analysis (DEA) model which allows for non-proportional adjustments to energy inputs and undesirable outputs and thus it provides different estimations for energy and environmental efficiency scores. The 2001–2008 time period was selected for this research. One of the most important findings is that countries like Germany, Sweden, or Austria, with strong environmental protection standards, appear to be less energy and environmentally efficient, compared with countries like Denmark, Belgium, Spain, France, or Ireland. In addition, a series of eastern European countries achieve low efficiency scores, which can be characterized as expectable, due to low technology level being implemented in the primary production process. There are also two sub-periods for this research. The first one (2001–2006) covers the fully coupled with specific cultivations period for subsidy administation, and the second (2007–2008) where the new decoupled subsidy scheme was implemented. There are significant hints for considerable changes of energy and environmental efficiency after the implementation of the the new CAP, with the new member states siginificantly differ of both energy and environmental efficiency copmared with the older ones.