The agro-industrial complex faces lots of challenges which brake its efficient economic, ecological and biological development and labor market functioning. Applying statistical analysis of the current indicators we estimate the influence of the negative factors and propose the possible solution. Despite its huge potential, the Russian agro-industrial complex is currently in a state of deep systemic crisis. The development of the agro-industrial complex is directly related to the quality of life of the rural population and the situation in the labor market. The possible solution is to develop engineering, social and transport infrastructure and improve the situation in the labor market in the rural areas. It is the state regulation and support of the agro-industrial complex that is currently the fundamental point of solving existing problems. To maintain efficiency in the agricultural sector, state regulation and support are not just necessary, but unavoidable. For effective operation and systematic development of the agro-industrial complex, it is necessary to form a program of state support for the sector in order to attract investment and innovation.