Reducing rice production costs is an urgent issue in Japan. To address this need, we conducted this study to quantify the cost reduction effect that could be obtained by improving operation skills, based on an empirical model developed using mathematical programming method. We focused on the cost that resulted from an optimal farming plan developed using the farming-systems analysis and planning support system (FVS-FAPS), which includes management resource constraints and the risks imposed by fluctuating weather. In addition, we performed a budget analysis to compare with the results produced by FVS-FAPS. We used three scenarios of beginner, intermediate, and expert in the analysis. Improving operation skills from beginner to intermediate decreased the cost by 29.5 percentage points, with a further improvement of 4.4 percentage points by improving operation skills from intermediate to expert. Our results suggested that improving operation skills can reduce costs in an optimal farming plan, and these results were confirmed by the budget analysis. We therefore recommend improved training for workers with low skill levels to reduce the costs of rice production.