Agro-industrial complex - a set of interrelated sectors of the economy involved in the production, processing of agricultural products and bringing it to the consumer. Agriculture occupies a special place in the life of the region, as it provides food and consumer goods. The development of agriculture significantly affects the level of national welfare, as its products account for about 60 % of goods in trade. The authors assess the current conditions and problems of agro-industrial complex of Tomsk region, determine the prospects of development of the complex, based on the implementation of the economic mechanism of sustainable development. A number of problems of development of agro-industrial complex in Tomsk region are revealed, some ways of its improvement are offered. The solution of problems of development of agro-industrial complex will contribute to the food security of the region and the country as a whole, focus on meeting the demand of the domestic market and increasing exports, improving the level and quality of life of the rural population.