Dynamic development and penetration on the market of modern information technologies and global databases create new prerequisites for cooperation of business and science every year. Creation of cluster initiatives in Russia becomes rather widespread way of achievement of competitive advantages in recent years, especially it is actual for basic branches of economy. Cooperation process of science and business aimed at innovative development, creation of new combinations of productive forces and means of production that leads to cumulative growth the regional and branch assets. However, traditional commitment of the State to make clusters of the enterprises by method «from above» and formalizations of processes and procedures doesn't allow to create identical conditions for all organizations of branch, to provide development of joint innovative activity of business. In this article is provided the analysis of institutional problems of the Russian economy which act as the factors weakening aspiration of the organizations to interaction, are brought the recommendations about their resolution.