Intensive rice production has contributed to feeding the world's growing world population, but it has also increased fossil energy consumption. This paper examines the effect of increasing the scale of rice farming on the energy efficiency of intensive rice production in Japan. A data envelopment analysis (DEA) approach is used to calculate energy efficiency scores and identify operational targets. A window analysis technique is applied to the 2005-2011 statistical data, with nine scales of rice farming, ranging from <0.5 ha to ≥15 ha. Six energy inputs (fossil fuels, electricity, chemical fertilizers, pesticides, agricultural services, and agricultural machinery) and the weight-based rice yield are selected as the DEA inputs and the DEA output, respectively. The results show that the energy efficiency scores range from 0.732 for farms of 1 ha to <2 ha, to 0.988 for farms ≥15 ha. Overall, increasing the scale of rice farming in Japan improves energy efficiency because of a great reduction in the energy consumed per unit area by agricultural machinery and agricultural services. These findings suggest that increasing the scale of farming is an effective way to enhance the energy efficiency of highly mechanized rice production in developed countries, such as Japan.