The article analyses national projects as a key element of the Russian territorial administration system and reviews management tools of regional and municipal executive authorities. The object of research is a system of territorial management. The subject is the peculiarities of the program and municipal methods application in a territorial management system. The goal is to determine the nature of the territorial administration system transformations and the role of municipal instruments in it. The authors use methods of systematic historical and institutional analysis. After systemic transformations, national projects are adapting to new economic and political conditions. Municipal instruments are relevant measures that have not yet been applied at the federal level, or have been applied to a limited extent. Regional or municipal authorities independently develop measures to improve management processes, which can later be applied at the federal level. Often such initiatives are designed to promote government transparency, establish communication channels between the state and society, optimize the interdepartmental interaction, improve the state institutions' tools of information and data management, etc. The key disadvantage is differences in the results due to lack of a unified approach to their application.