In scientific work the peculiarities of innovation processes in the activity of high-tech companies are determined. The functional and managerial components of ensuring the security of development of high-tech companies are determined on the basis of establishing centers of responsibility for the support of innovative projects. The model of support of sustainable innovation development is developed and the algorithm of formation of the structure of business of high-tech companies with the purpose of strengthening of organizational security of out-of-date development is offered. The recommendations on harmonization of innovation development and security of commercial activity for high-tech companies are given.