The article describes technical and economic issues of providing defense potential in the aerospace sector under in conditions of increasing military and technological challenges and threats and implementing the strategy of import substitution. The paper presents analysis of the information-technological problems of development of domestic military-industrial complex enterprises — developers of aerospace defense systems, it identifies reserves for increasing their efficiency through introducing integrated information systems. On the example of “VNIIRT” JSC the paper presents prospects for implementing the lean manufacturing concept on the basis of product lifecycle management technology. It gives comparative characteristics of cooperation business models in the defense industry both in foreign countries and in Russia. The article identifies technological and organizational-economic factors of developing cooperation of the final integrators, sub-integrators and components suppliers in the military products manufacturing. It sets out system-forming elements of a risk-oriented approach to forming co-operation in the defense-industrial complex. The authors propose a mathematical model of risk indicator for the company-finalist when choosing the composition of enterprises participating in cooperation, based on aggregation of private indicators of scientific and technical, industrial and technological, financial and economic risks. They formulate long-term objectives for the proposed approach implementation with application of neural network technology.