Large tracts of farmland have been abandoned in rural areas of Japan. The resulting land use change is of concern for policy-makers not only because of its socio-economic consequences, but also because of its implications for the delivery of multiple ecosystem services. Public funding schemes have been established to counteract the trend towards land abandonment, e.g. the ‘Direct Payments for Hilly and Mountainous Areas.’ However, it is unclear how farmland abandonment affects the supply of different ecosystem services or how public funding schemes may influence the underlying ecological processes. Using public statistics and land-cover data, we examined (i) the spatial relationships between abandoned fields and ecosystem service supply, and (ii) the implementation of public payment schemes across the land. We hypothesized abandoned fields to occur in marginal areas where a range of ecosystem services are provided, and payments schemes to be optimal if distributed accordingly. Indicators of ecosystem services related to agriculture, the area of abandoned fields, and the amount of payments were collated at municipality level and subjected to correlation analysis. The results provide a quantitative basis for discussing the efficiency of payment schemes for rural areas in achieving policy goals related to the balanced provision of ecosystem services.