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Safety Management System (SMS) is the basis of new proactive concept of accident/incident prevention, which in methodological sense assumes risk identification within the latent phases of the potential accident/incident causal appearance. In comparison to the traditional approach, this concept features system analysis tools and failure detection within all segments and all levels of air transport governing – from regulator to operators of airports, airlines and air traffic management. For European transition countries, in regards to socio-economy status and strategic priority of regional development, safety culture development and safety management implementation have become precondition for their integration and competitiveness on international aviation market. Aggravating circumstance in this context is insufficient administrative capacity for regulation and oversight of safety standards implementation. This paper intends to elaborate the regulatory framework of SMS establishment, as well as the problems of SMS implementation in transition countries’ air transport operations. Finally, the applicative model of integrated SMS is suggested, which would balance the regulatory and operational safety processing of the air transport system in a synergic way.