Small farm size and high production costs pose major problems for Japanese rice cropping. We used the Farming-systems Analysis and Planning System database (FAPS-DB) to estimate the effect of improving farmers' skills and the effect of scale on the production costs of large-scale rice farming. At a scale of 150 ha, the cost per unit of production decreased to around 88% of those at a scale of 50 ha. In simulation analyses in which all operators are either beginners or experts, the cost per unit of production at a scale of 150 ha were 94% of those at a scale of 50 ha in the beginner scenario and 87% in the expert scenario. Thus, increasing experience is effective at decreasing production costs, especially fixed costs and labor costs. At a scale of 150 ha, a higher level of farming skill achieved a greater reduction of production costs. These results suggest that it is important to provide effective agricultural training in order to reduce production costs at the farm and national levels.