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The paper is concerned with the assessment of current trends in the development of Russia's innovative activity. Problems of the national innovation system performance at a regional level are revealed. The paper analyses the activity of the Special Economic Zone of technological development type “Tomsk” (SEZ) and universities in the field of innovations development and creation of necessary conditions for setting up a modern innovation center. A comparative analysis of the factors related to the theory of innovations, which provide the necessary conditions for creating a well-functioning innovation center, as well as the results of the performance of the above-mentioned subjects is conducted. The assessment of the innovative activity of Tomsk universities and the Special Economic Zone demonstrates the lack of provision of a number of conditions for the effective functioning of the innovation center in Tomsk. The results of the study demonstrate that it is necessary to make changes in the educational, research, and motivational activities of universities in terms of students in order to involve them in innovative activity. Universities should be encouraged to develop and implement an independent innovation strategy and participate in the work of the special economic zone in Tomsk.