Purpose <p>This study examined the decline in the number of surgeons in Japan compared with other specialists in urban and rural areas using a secondary analysis of government-owned census data. Furthermore, it evaluated the impact of the regional quota system in addressing the shortage of surgeons by comparing their proportion among the graduates of this system with that of the overall physician population.</p> Methods <p>We analyzed national census data (2012–2022) to evaluate trends in the numbers of physicians and surgeons in 47 prefectures from urban and rural groups. Data on regional quota graduates were obtained from an open-source study.</p> Results <p>The number of physicians increased by 13.4%, whereas the number of surgeons decreased by 2.1%. The change in the number of surgeons per 100,000 population did not differ between the rural (+ 0.6%) and urban (+ 0.7%; p = 0.997) prefectures. Regional quota graduates had a higher likelihood of being surgeons (9.5%) than all (8.2%; p &lt; 0.01) or young (age 26–39&#xa0;years) physicians (7.8%; p &lt; 0.01), although female representation was highest among regional quotas (38.7%) relative to all (22.8%; p &lt; 0.01) and young (32.8%; p &lt; 0.01) physicians.</p> Conclusion <p>The regional quota demonstrates the potential of addressing surgeon shortages.</p>