Introduction. For effective implementation of the state innovation policy is necessary to form a new model of the relationship of the triad «state – business – science» in the innovation system on the principles of the concept of «triple helix». Empirical Analysis. The results of the analysis of the survey of professionals involved in the implementation of programs of the National Research Universities aimed at studying the authoritative opinions of experts about the possible directions of development of ways of interaction of universities, government and business to improve the efficiency of the innovation system in Russia. The analysis of the distribution of roles by the participants of the innovation process, which allowed to determine the positive trends and to identify the main risks and threats in the course of implementation of the development of national research universities. Results. Main directions of formation control strategy for enhancing the role of the National Research Universities in the innovative development of the region: building relationships with business entities in any way possible; self-independent development of the National Research Universities in all directions; working closely with the development objectives of the state and the region and deepening links with regional and international partners to implement these strategies.