Food and nutrition security relies on the safe, affordable, and nutritious supply of fresh and processed foods to all individuals. Japan has set a national target to halve food loss and waste by 2030 compared to the year 2000. Various initiatives have been implemented to reduce the disposal of potentially edible food and make the food sector more resource efficient. These efforts include reintroducing potential food loss and waste from farms and production side-streams back into the food chain or repurposing them for other food sources. For instance, the utilization of food banks and the consideration of using upcycled foods print cartridges to utilize food loss and waste are being explored. To address these challenges and ensure the sustainability of the food supply chain, it is important to understand the flow of food and nutrition in Japan. Therefore, this study utilized material flow analysis to illustrate this flow and calculated the reuse rate of food loss required to compensate for nutritional deficiencies in Japan. By providing new insights into designing a sustainable food supply chain, this research contributes to the advancement of food and nutrition security and offers valuable suggestions.