In the wake of the Fukushima nuclear disaster, Japan largely moved away from nuclear power generation and turned back towards an energy sector dominated by fossil fuels. As a result, the pace towards reaching emission reduction targets has largely slowed down. This situation indicates that higher emissions will continue to be generated if there is no appropriate and efficient measurement implemented to bridge the energy demand gap. To contribute adequate mitigation policies, a detailed inventory of both CO2 emissions and socioeconomic factors, both at the national and regional level, should be issued. Thereby, this work contributes to a time-series emission with a record of 47 prefectures in Japan as well as their associated socioeconomic features. The compiled emission inventory is based on three major fossil fuels and 26 sectors with careful emission allocations for regional electricity generation. This dataset is uniformly formatted and can be expected to provide vital information to set regional reduction allowances and sectoral reduction priorities.