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The innovative transformation of the Russian economy is the systemic tool that could help the Government of the Russian Federation to ensure the national competitiveness in the long term and to solve successfully the accumulated problems in the social and economic sphere. However, at present, there is no continuous chain of value creation in Russia at all stages of its implementation (from the order for research and innovative development to their implementation into production and the creation of innovative companies). As a result, the implementation of R & D into the production and the commercialization of innovative ideas are more like the exceptions rather than the rule in the current system of innovation administration The existing systemic and sectoral problems on the way to the introduction of innovative medicines on the market were identified. The necessity of adjusting the state policy in the field of innovations was proved. At the same time, one of the major sectoral problems is the imbalance in financing of the drug development stages: 1) There is a significant excess of applied research over search and fundamental research, which is caused by a low probability (0.35%) of conversion of the active substance into a drug that grows as the results are transferred to the next stage of the life cycle, and only after the phase III clinical trials Will be 65% [1]: 2) There is a lack of funding for applied research and R & D aimed at developing methods and technologies for the production of pharmaceuticals and pharmaceutical substances. At the same time, technologies for obtaining active pharmaceutical substances by local producers are needed for the needs of national markets, with the following advantages: The lowest operating costs, repeatability, stability and safety of production processes; Low capital costs due to the compactness of production site; Low capital costs due to the high safety of the production method itself [2]. 3) Lack of support for clinical trials influences on the results of preclinical studies that are actively supported by the state in recent years - they remain unclaimed. Given the continuing potential and competitive advantages of Russian science, these negative factors and trends create the risks of Russia's lagging behind countries-world technological leaders and the devaluation of domestic investments in science and technology, reduce Russia's independence and competitiveness in the world and jeopardize national security. In the context of significant restrictions on other opportunities for the development of the Russian Federation, these risks and threats become a significant barrier that hinders the long-term growth of society's welfare and the strengthening of Russia's sovereignty. References [1] Lin A.A., Goncharov V., Ivichev E.A. – The field of pharmaceuticals is the most high-technology part of world economy // SEI GESUND. – 2016. – №1. – P. 23-25. [2] Narkevich I.A., Semin A.A., Kartashova N.S., Teslev A.A. Pilot and Industrial Sorption Chromatography and Membrane Technologies for the Isolation and Purification of Plantand Animal-Based Active Pharmaceutical Ingredients – 2016. – Т. 50. № 10. – 54-60 p.