This paper presents a case study to show how beneficial a regional concentration of waste treatment and disposal is. The key method, an inter-regional counterpart of the waste input-output linear programming model (Kondo and Nakamura, Economic Systems Research, 2005), is developed, and applied to the 1995 Japanese 9-region inter-regional waste input-output table. One of the important problems to solve in Japan is the shortage of landfill site, which is partly due to the uneven distribution of landfill sites. The results indicate that, at the cost of the increase of CO2 emission only by 0.2%, the shortage of landfill site in some regions is alleviated by regional concentration. It is expected that the developed method can support realistic decision-making about the regional strategies of waste management.