The article considers an important priority of the state policy of the Republic of Kazakhstan – the preservation and strengthening of public health. In the context of this problem, the quality of management of medical institutions plays an important role. In the context of the economic crisis in health care, it is necessary to increase the efficiency of medical institutions through the introduction of new forms, methods and models of management. Factors that make it difficult to manage health organizations can be divided into two groups according to the method of occurrence: environmental factors and internal environmental factors. Together, interacting with each other, these factors lead to inhibition of the development of modern medicine. Thus, it is possible to identify the main problems that arise in the management of medical institutions at the present stage: the fragmentation of underfunding, low level of confidence of Kazakh citizens in the health care system, the problems of quality and availability of medical services, the lack of highly qualified medical personnel, low managerial skills of heads of health organizations. Conclusions on improving the quality of health services are made.