Objectives In this longitudinal study, we examined changes in the geographical distribution of physicians in Japan from 2000 to 2014 by clinical specialty with adjustments for healthcare demand based on population structure. Methods The Japanese population was adjusted for healthcare demand using health expenditure per capita stratified by age and sex. The numbers of physicians per 100 000 demand-adjusted population (DAP) in 2000 and 2014 were calculated for subprefectural regions known as secondary medical areas. Disparities in the geographical distribution of physicians for each specialty were assessed using Gini coefficients. A subgroup analysis was conducted by dividing the regions into four groups according to urban-rural classification and initial physician supply. Results Over the study period, the number of physicians per 100 000 DAP decreased in all specialties assessed (internal medicine: -6.9%, surgery: -26.0%, orthopaedics: -2.1%, obstetrics/gynaecology (per female population): -17.5%) except paediatrics (+33.3%) and anaesthesiology (+21.1%). No reductions in geographical disparity were observed in any of the specialties assessed. Geographical disparity increased substantially in internal medicine, surgery and obstetrics and gynaecology(OB/GYN). Rural areas with lower initial physician supply experienced the highest decreases in physicians per 100 000 DAP for all specialties assessed except paediatrics and anaesthesiology. In contrast, urban areas with lower initial physician supply experienced the lowest decreases in physicians per 100 000 DAP in internal medicine, surgery, orthopaedics and OB/GYN, but the highest increase in anaesthesiology. Conclusion Between 2000 and 2014, the number of physicians per 100 000 DAP in Japan decreased in all specialties assessed except paediatrics and anaesthesiology. There is also a growing urban-rural disparity in physician supply in all specialties assessed except paediatrics. Additional measures may be needed to resolve these issues and improve physician distribution in Japan.