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The article considers the processes of forming the strategic system of innovative activity management at the enterprises of a high-tech mechanical engineering complex (MEC) that are traditionally decisive in shaping the economic base of Russia. The authors proposed a method of designing a strategic system of innovative activity management at the MEC's enterprises of the region which is based on the consideration of means and opportunities of the enterprise to implement intellectual activity. The proposed methodology and the empirical results constituted a ground for developing a system of strategic innovation management when performing the state-guaranteed order at the hi-tech MEC enterprises. Its implementation will help to reduce the level of uncertainty throughout the entire life cycle of an innovative activity product.