In the context of the weakening economic development of the region, it is necessary to find new ways to increase the efficiency of interaction between the economic structures of the region. One of the areas is the development of integration processes in the field of cooperation between the public and private capital to meet the goals and objectives of the effective functioning of both the participants of integration interaction, as well as the region as a whole. Factors that influence the emergence and development of integration processes, are a scarce resource; motivated by the need to diversify the business; the desire to improve the economic efficiency of business entities. Development grace-integral process is economic interaction managing subjects, followed by combining them to achieve common objectives and obtain the synergistic effect due to a number of resource solutions, organizational and administrative problems. To obtain high economic benefits of integration interaction of the participants, we have proposed a mechanism for the development of integration processes in the region, based on three levels of interaction between regional authorities, educational institutions and private organizations. It allows forming a single chain integration and process management to increase the effectiveness of their implementation in practice, and to avoid the disadvantages associated with the formation of the integrated structures. Integration cooperation of regional authorities with organizations of various spheres of activity of the region and education (research) organizations is a key component of the new Russian innovation policy because, if done right, it provides broader benefits from investments in research and development, creating favorable conditions for sustainable innovation development and is a strategic factor in the economic growth of the region.