Background. The solution to the problem of food security of the Russian Federation is possible only the through the prism of the development of innovative agroekonomika. The materials and methods. The experience of the protectionist policy of the Western States, leading to a substantial reduction in national agri-food complexes in the countries with economies «catching-up». The characteristic of the basic tools of influence on them. A retrospective analysis of the formation mechanism, aimed at protecting the domestic food market of Russia. Results. Based on the study of Russian legislation there are revealed the possibilities of innovation in agriculture in contrast to the prevailing view on innovation as an exclusive prerogative of industrial production. Clarifies the definition of the mechanism of ensuring food security, given the specifications of the conditions of Russia. Studied the economic and administrative instruments stimulating import substitution and factors of increasing efficiency of their impact. Conclusions. If you do not ensure accelerated development of the private sector of the agrarian economy that define its specialization in the global systems of management and allowing to the greatest extent to realize the national competitive advantage, it is impossible to achieve efficiency of production and food sovereignty.