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The article presents methodological recommendations for managing the innovative development of complex socio-economic systems in the context of movement towards the information society, the formation and development of problem-oriented information and communication social spaces, the formation of specialized virtual innovation clusters, the organization of effective interaction between government bodies and local self-government, economic entities, their associations, other organizations and citizens having common interests and a common goal. The proposed methodological recommendations and model of innovative development can, with account of specific features, be effectively applied in various sectors of the national economy. Using the research results in practice will contribute to solving the problem of innovative modernization of the country, adapting authorities, organizations and citizens to the conditions of the global information society, increasing the functioning and competitiveness of complex socio-economic systems, improving quality and increasing the volume of socially significant products. An intelligent control system is proposed and a technology for managing the innovative development of complex socio-economic systems is developed.