Farmland abandonment has been a serious problem in marginal areas in Japan. One of the main disadvantages of farmland abandonment is the effects of negative externalities on the adjacent farmlands, such as increased insect damage, weed growth, and maintenance costs of common facilities. In this paper, an empirical application of a linear programming model is introduced, which can deal with unknown values of negative externalities caused by adjacent abandoned farmlands. The unit cost of externalities caused by farm abandonment is calculated through observed land use and farming practices. The optimized result is able to reproduce the observed land use pattern at a significant hitting ratio. By substituting calculated value into the model of current cropping plots, we can suggest the optimal land use plan for the limited labour input in the changing future. The farmland plots in the suggested land use plan are not scattered spatially, reflecting the effect of externalities.