Energy security and food security are two key policy objectives of the Japanese government. However, their study and the policies that have targeted them have been disjointed at best. This paper explores the links between these two policy objectives by quantifying the resources used in (a) the agricultural sector as a whole and (b) two very resource intensive sub-sectors, beef and pork production. Emergy synthesis is used as the analytical approach for the period 1975-2005 with the results suggesting that not only is more natural capital currently being used within the agricultural sector but the efficiency of the agricultural production has declined considering the increase in transformity during the same period. What is more important though is that agricultural yield is strongly correlated with resource use (quantified as emergy). This finding suggests that sudden changes in resource supply can affect agricultural production and as an extension national food security. Overall the evidence presented in this paper shows that energy security and food security are indeed interconnected and that integrated policy responses will be required if these issues are to be tackled effectively. (C) 2010 Elsevier Ltd. All rights reserved.