The author recognizes that the search of new approaches to management is necessary for providing the Municipal Healthcare System with sustainable development of medical institutions. The author finds out the factors of the internal and external environment, restrictions and conditions, influencing the processes of formation of mechanisms of programme management for the development of the organizations of the medical sphere. The activity of the leading Russian organizations of the medical sphere was analysed. It was proved, that these organizations has low medical and economic efficiency, when forming their mechanisms of programme management for the development of the organizations of the medical sphere. The author has developed some recommendations for the improvement of processes of formation of mechanisms of programme management, in order to provide the organizations of the medical sphere and the Municipal Healthcare System as whole with sustainable development. At the same time, the importance of such development for social stability and comfort of cities is emphasized.