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The present article addresses the issue of integration of higher professional education establishments, science and industry in Russia. The basis for collaboration of these institutions is national research universities with academic research establishments and different operational sites for the purposes of implementation of overall reform of education system in the Russian Federation. The strategic framework for integration of science, education and industry in modern society and main reasons and targets for improvement of their collaboration on the basis of new development paradigms of modern democratic society have been described. It is found that integration of science, education and industry based on higher education establishments is a multi-level process, which includes the development of international cooperation of global information medium, uniform educational space and use of different innovative techniques and methods of teaching. The article is based on the study of educational activity of two national research universities - Tomsk State University and Tomsk Polytechnic University, which serve as central integration platforms for Tomsk research and educational complex. Main directions of their work for improvement of educational activity aimed at intensifying the efforts of science, education and industry to increase the competitiveness of Russian innovation technologies have been explored in the present article. As the article highlights, Tomsk model of integration of education, science and industry at the present stage of its development shows real benefits for the economic development of Tomsk region.