Preservation and restoration of the natural environment and ensuring environmentally safe functioning of ecosystems are the priority conditions for implementation of the dominant social paradigm, which is development in harmony with nature. The article describes the essence of management system of ecological safety of territorial units as a set of actions and processes aimed at planning and constructing optimum options of spatial-temporal structuralfunctional organisation of ecosystems, restoration and increase of their ecological potential and stability, prevention of occurrence and development of ecological risks. Structure blocks of the system are environmental audit, environmental design (planning), environmental monitoring, databases and data banks with the use of GIS technologies. Implementation of the ecosystem services concept has an important role in the management system of ecological safety of territorial units. It is based on the need of co-evolution development of ecological and economic components. Monetary evaluation of the ecosystem services, development and introduction of payment mechanisms for these services will allow implementing programs (measures) for ensuring environmentally safe functioning of ecosystems within the territorial units.