An embodied CO2 emissions intensity database estimated from input–output data at current prices is now available in Japan. This study compares two non-survey methods: The double-deflation (DD) method and an elaborated approach combining the DD method with the generalized RAS method to deflate an input–output table (IOT). We used these methods to estimate new datasets of embodied CO2 emission intensity data in Japan, utilizing Japan's IOTs for 2005, 2011, and 2015 at constant prices in 2015. Furthermore, we compare the estimated data of 367 commodity sectors for a specific year (2005 or 2011). The results reveal that the intensity for certain aggregated sector groups, such as non-ferrous metals and finance and insurance, exhibits higher uncertainty owing to the extreme price homogeneity assumption associated with the DD method. Consequently, we recommend that life-cycle-assessment practitioners use an open database when analyzing changes in the carbon footprint of products over time.