Introduction. National research universities, created in Russia in 2009 to improve the quality of Russian education, the integration of research and development of innovative economy, play a key role in the generation of new knowledge, a comprehensive transformation of innovations and translate them into real projects with the goal of launching innovation across all business sectors in cooperation with the authorities of the regions. Еmpirical analysis. Presents the results of a study of the opinions of specialists and experts involved in the implementation of the National research universities programs on existing relationships, mutual influence and the factors of interaction between universities, government and business in regional innovation systems. A significant aspect of the research were to factor into account the regional context of the needs and interests of the region in the plans and programs of the university, as well as the study of existing mechanisms of cooperation and active links between universities and representatives of the regional industry and government. Results. Major factors that facilitate or hinder the development of cooperation of regional actors: universities, government and business in regional innovation systems. There have been positive current opportunities National research universities, developed since the implementation of the programme of support to universities, as well as difficulties with the legislative and regulatory regimes and funding issues.