The author has identified a low level of innovative development of the agroindustrial complex and the reasons for the delay in its growth in comparison with other industries and types of economic activity in Russia. The consequence is a noticeable trend of changes in the positive dynamics of economic efficiency indicators of agricultural production in the recent past. This trend indicates weakening Russia’s food security. The article considers one of the possible options for import substitution of innovative means of production used in the agroindustrial sector in the conditions of external economic isolation of the country. It implies the participation of the state in supporting the development and assimilation of knowledge embodied in the real economy as well as in the financing of national innovative solutions. The option under consideration has the following features: selection on a competitive basis and priority financing of means of production with a high technological potential, which are most in demand among agroindustrial enterprises; reimbursement of payment for information on the state of the markets for technology, means of production, resources, food, raw materials provided by IT specialists, as well as for making calculations to optimize the structure and volumes of production, product exports and technological training to enterprises. This kind of financial support is provided in addition to the current practice of state compensation for losses to low-profit agricultural businesses. An experimental scheme for making decisions on priority financing of innovations is examined. The creators of these innovations are economic entities with the highest indicators of production activities and a high probability of fulfilling an order for the output of innovative products. The list of indicators includes many quantitative and qualitative characteristics. This means that the problem is classified as one that can be solved by using algorithms of multiple criteria modeling.