BACKGROUND: Shortages and imbalances in physician workforce distribution between urban and rural and among the different regions in Ethiopia are enormous. However, with the recent rapid expansion in medical education training, it is expected that the country can make progress in physician workforce supply. Therefore, the aim of this study was to examine the distribution of physician workforce in Ethiopia and assess the role of retention mechanisms in the reduction of physician migration from the public health sector of Ethiopia. METHODS: This organizational survey examined physician workforce data from 119 hospitals from 5 regions (Amhara, Oromia, Southern Nations Nationalities and Peoples Region [SNNPR], Tigray, and Harari) and 2 city administrations (Addis Ababa and Dire Dawa City). Training opportunity, distribution, and turnover between September 2009 and July 2015 were analyzed descriptively. Poisson regression model was used to find the association of different covariates with physician turnover. RESULTS: There were 2,300 medical doctors in 5 regions and 2 city administrations in ~6 years of observations. Of these, 553 (24.04%) medical doctors moved out of their duty stations and the remaining 1,747 (75.96%) were working actively. Of the actively working, the majority of the medical doctors, 1,407 (80.5%), were males, in which 889 (50.9%) were born after the year 1985, 997 (57%) had work experience of <3 years, and most, 1,471 (84.2%), were general practitioners. Within the observation period, physician turnover among specialists ranged from 21.4% in Dire Dawa to 43.3% in Amhara region. The capital, Addis Ababa, was the place of destination for 32 (82%) of the physicians who moved out to other regions from elsewhere in the country. The Poisson regression model revealed a decreased incidence of turnover among physicians born between the years 1975 and 1985 (incident rate ratio [IRR]: 0.63; 95% confidence interval [CI]: 0.51, 0.79) and among those who were born prior to 1975 (IRR: 0.24; 95% CI: 0.17, 0.34) compared to those who were born after 1985. Female physicians were 1.4 times (IRR: 1.44; 95% CI: 1.14, 1.81) more likely to move out from their duty stations compared to males. In addition, physicians working in district hospitals were 2 times (IRR: 2.14; 95% CI: 1.59, 2.89) more likely to move out and those working in general hospitals had 1.39 times (IRR: 1.39; 95% CI: 1.08, 1.78) increased rate of turnover in comparison with those who were working in referral hospitals. Physicians working in the Amhara region had 2 times (IRR: 2.01; 95% CI: 1.49, 2.73) increased risk of turnover in comparison with those who were working in the capital, Addis Ababa. The probability of migration did not show a statistically significant difference in all other regions (>0.05). CONCLUSION: The public health sector physician workforce largely constituted of male physicians, young and less experienced. High turnover rate among females, the young and less experienced physicians, and those working in distant places (district hospitals) indicate the need for special attention in devising human resources management and retention strategies.