The need to develop horizontal type cooperation as the basis of integration ties between enterprises of related sectors of AIC of Kazakhstan has been justified. The establishing of medium and large commodity productions and cooperative entities plays an important role. In establishing cooperatives based on the unification of small peasant farms of population, it is important to determine the optimal production structure which ensures the effective use of the resource potential and achievement of maximum profitability level. The article shows the ways of addressing this problem based on the use of economic-mathematical model. An important issue is the unification of small commodity producers and large processing enterprises into cooperatives. Correspondingly, the issues of regulation of interaction ensuring equal and mutually beneficial partnership, compliance with obligations in supply of raw materials and implementation of payments have been considered. Other issues related to the organizational and economic prerequisites for the development of cooperation in agricultural sector of the republic have also been revealed. The article contains the research results on grant financing for 2015-2017 in the budget program 217 "Scientific Development", sub-program 102 "Grant funding for research" on the project topic: No. 5467 / GF4, registration number No. 0115RK01913.