This study investigated the factors behind the historical changes in CO 2 emissions of the Japanese manufacturing industry as a whole and by sector at the prefectural level. We decomposed the changes of CO 2 emissions in 47 prefectures from 1990 to 2013 into four factors (carbon intensity, energy intensity, structure, and activity effects) using the logarithmic mean Divisia index method. We found that energy intensity, structure, and activity effects were more influential in the changes of emissions than the carbon intensity effect, although the most influential factor varied by prefecture. Among the eight considered industrial sectors of Japan's manufacturing industry, the changes in the chemistry and metal sectors were particularly complex. Thus, improvements of the energy intensity and production in these two sectors should be prioritized. We also conducted detailed analysis of the decomposed factors in three selected prefectures based on cluster analysis.