OBJECTIVES: To contribute to the informed debate about the determinants of medical salaries in the public health sector in a middle-income country under a decentralized health system context. METHODS: A multiple response questionnaire was developed for 631 physicians in 25 public health institutions in 5 Argentine cities: Buenos Aires City, Salta, La Rioja, Chaco and Neuquén, in the year 2014. By means of the estimation of a ordered multinomial logit model we identified the personal, union and institutional determinants, among others, that explain the salary levels perceived by the doctors surveyed. RESULTS: The length of the working day, the presence of a medical specialty and the years of experience in the institution by the physician show positive signs, and are statistically significant, when explaining the salary levels perceived. Having a labor contract with contributions and working at the Hospital Materno Infantil de Salta (private management) are associated in a positive and statistically significant way, while the gender of the physician does not seem to be associated with the remunerative level. On the other hand, the union action variables show a positive sign and are statistically significant in the income level of medical professionals. CONCLUSIONS: A salary scheme that is aligned with the technical knowledge, effort and motivation of medical professionals in the public health sector is of great importance in order to achieve an equitable and efficient health system. The results obtained here contribute to the informed debate on wage policy in health in a context of middle-income countries, although more research is needed.