Introduction: Managers of health service providers´ institutions must make timely and sound decisions, and appropriately identify their main problems, to propose improvement actions in the management of their institutions. Objective: Identify problems in the management of health facilities in Peru from the perspective of their managers according to the ENSUSALUD 2016 survey. Methods: A secondary descriptive analysis of the ENSUSALUD 2016 survey database was performed. Data of persons in a managerial position at selected health service providers´ institutions were analyzed. Results: 366 people with a management position were interviewed in 184 Peruvian public and private sector health service providers´ institutions and different levels of care, from 25 regions. 68.03% of respondents were male and 52.73% were doctors. The average age was 48.62 (±11.10) and with an average of 11.7 (±10.45) years working in the health institutions and 4.60 (±6.63) in a managerial position. Nearly half of managers (43.7%) mentioned that the main management problems at the regional level are the human resources deficit, the budget deficit (38.2%) and specialists deficit (34.7%). Conclusions: The main problems identified by managers of health facilities are the scarcity of human resources, the lack of inputs and medicines, the poor infrastructure and the budget deficit. These results provide useful knowledge for health managers and decision makers who have the responsibility to make informed and timely decisions to improve the quality of services and user´s satisfaction.