This study evaluates the progress of efficient energy use and the control of carbon dioxide (CO2) emissions in Japan between 1990 and 2012. A new indicator of energy performance is presented called environmental energy efficiency (EEE). The EEE of manufacturing industries was measured by each prefecture in Japan. We estimated the influencing factors of EEE for each industry by applying the pooled mean group (PMG) method. Our findings are as follows: First, the Japanese manufacturing industry has not been in line with the EEE improvement goals since the adoption of the Kyoto Protocol. However, the progress of each industry was relatively consistent by region. Second, EEE tends to improve and then deteriorate or monotonically increase as economic development progresses. Third, EEE is raised by expanding industry share. Finally, EEE, which focuses on energy reduction, is likely to increase with the progress of energy-saving technology.