Abstract-The article is devoted to the existing forms of government, business and science cooperation in innovation economy sectors at the regional level and to the possibilities of applying the concept of "triple helix" and its multi-helix modifications. Russia needs a correction of economic imbalances, improving the institutional environment and reforming the system of regional development management. The article reveals the most perspective forms of interaction of government and business: agreements on public-private partnership, concession agreements, special investment contracts. The key issues of embedding science in these chains are specified and the solutions to these problems are proposed. Changes in Russia will require overcoming the existing gaps in three dimensions: firstly, at the level of education and science where an innovative generation (people with imagination) should be formed. Secondly, at the enterprise level, where changes will require building the relations between fundamental and applied interdisciplinary research on the one hand and introduction of the developments into production on the other hand, contributing to the achievement of a balance between international innovation and tradition.