The article analyzes the development of the system of departmental management of closed cities in Russia in the period from the 1940s to the 2000s. For convenience, the temporary frames of the study are divided into three periods: the first dated 1945-1954, the second is 1954-1991, and the third period, which dates back to 1991, continues at the present stage and is relevant to the study to this day. At each of these periods, the main features of the system of departmental management of closed cities at the Federal, regional and municipal levels were highlighted. The analysis of the departmental management system is based on the normative legal acts issued by the Presidium of the Supreme Soviet of the RSFSR in the Soviet period, and the government of the Russian Federation in the post-Soviet period. The results of the work revealed a specific way to establish a departmental structure for managing closed cities, with a number of features characteristic of secret territories.