The paper examines the prospects for import substitution in high-tech industries of Russia’s agro-industrial complex (AIC). It aims to identify and assess the factors behind the priority of import substitution policy. The research employs the methods of economic-statistical and correlation analysis. The results show that there are four types of government support that exert the most profound effect on import substitution in mechanical engineering and the AIC sectors based on high technologies and innovations. These are compensation for direct costs incurred in the construction and modernization of the AIC facilities; investment lending in the AIC; soft loans for the AIC enterprises; and the creation of the Center for the Analysis of Agricultural Products Export (Prod.Center). The study highlights the major challenges and avenues for import substitution in the Russian agro-industrial complex. The results obtained can be used when formulating a development strategy for high-tech agricultural sub-sectors and forming industry-specific and regional development programs. © 2020, World Scientific and Engineering Academy and Society. All rights reserved.