The article examines current issues of inter-industry economic relations using the example of the dairy and product subcomplex as the most problematic in the agro-industrial complex. Based on a systemic analysis, it was revealed that the violation of cost proportions between technologically interconnected agricultural organizations, processing enterprises and the trade sector is the main reason for the crisis in dairy cattle breeding, a sharp decrease in the number of cows and, as a consequence, a shortage of milk and dairy products in our country. Therefore, the regulation of economic relations in order to create equal (equal) business conditions for all participants in the reproduction process and, first of all, agricultural dairy organizations in this study is presented as the main imperative for the effective functioning of the entire agro-industrial dairy and food subcomplex of Russia. All this is aimed at increasing the milking population of cows and increasing the volume of domestically produced milk, which will ultimately fill the Russian market with its own dairy products at the level of quantitative parameters adopted by the Doctrine of Food Security of the Russian Federation.