It has been observed that market failure has hampered the development of sustainable forest ecosystem services such as CO2 absorption and fixation, water retention, and biodiversity. One of the reasons for this is that the link between forest land use and the beneficiaries of that use has not been widely recognized or clearly established. To address this problem, we conducted a footprint analysis to clarify the linkage between Japanese taxpayers as the beneficiaries of forest land use and the use of tax revenue and monetary donations for forest management. This study focuses on how the current forest tax collected from Japanese taxpayers (63 billion Japanese yen) could be allocated more fairly. The question of whether the collected taxes are sufficient is left for another time. At the core of our analysis, we examined the carbon footprint and established a linkage between the origins of CO2 emissions in Japan and their destinations by using a subnational multiregional input-output database and building a base table focused on various land use types and subnational regions at the municipality level. By clarifying these linkages and enhancing their transparency, we provide a basis for developing alternative financing schemes involving both taxation and taxpayer donations in support of forest management activities and protection of biodiverse habitats.