Recently, the Japanese government has introduced ambitious policies for agricultural sustainability, specifically the MIDORI Strategy, aimed at reducing chemical fertilizer use, expanding organic farmland, and increasing calorie-based food self-sufficiency. To evaluate the feasibility of these goals, this study quantified nitrogen and phosphorus flows within the 2021 food and feed system using a normalized “Nutrient Index.” A scenario analysis was conducted using policy targets as parameters, where currently non-circulated waste streams were modeled as potential sources for domestic nutrient recovery. The results indicate that Scenario A (a 30% reduction of chemical fertilizers) is the most feasible, achieving significant improvements in circulation ratios through recovery of nutrients from sewage and livestock waste. While Scenario B (increasing organic farmland) shows similar trends, its success depends on technological advancements to mitigate the yield gap between organic and conventional systems. Scenario C (increasing calorie-based food self-sufficiency) presents the greatest challenge: maintaining current dietary patterns requires a 20% expansion of farmland and total nutrient recovery from waste. However, shifting dietary habits toward higher domestic rice consumption (Scenario C-2) significantly mitigates land and fertilizer demand. Achieving these targets requires a holistic approach that integrates technological infrastructure with socio-political shifts in land use planning and consumer behavior.