This paper describes the concept of closed administrative-territorial formations (CATF) development. Solution of the problems described in the article the author sees in the system approach, including general organizational issues regarding CATF both in legal and economic aspects, as well as technological planning, viewed in the format of the innovation system. It is proposed to form a basis for the innovative economy construction in the format of the state strategic planning of the nuclear industry with active use of industrial sites throughout the whole CATF system.