At the present stage of production development innovation-active enterprises made the transition to network organizational structures. They often abandon the full cycle of production of innovative products and become system integrators of final products or specialized suppliers of components, working in the interests of various system integrators. The creation of the innovation infrastructure of the parent enterprise is associated with the risks inherent in network organizational structures, such as indirect competition with other system integrators that create the final product, which can be used by specialized supplier enterprises. In addition, a significant obstacle to the formation of the innovation structure of the system integrator is the high risk of investing in innovation. Therefore, there is a problem of coordination of innovative strategies of integrators and the enterprises-suppliers of components at joint implementation of innovative activity. This article is devoted to the solution of this problem.