The paper proposes a toolkit for assessing economic security based on a multi-level system of indicators of economic security, threshold values of indicators. The toolkit was developed on the basis of a theoretical synthesis of scientific approaches and economic and statistical methods for assessing economic security. A comparative assessment of the economic security of the eastern regions of Russia for 2010 and 2016 is given, the risks and threats to industrial, food, innovation, financial and social security are identified as constituting the main components of the economic security of the border region. The conclusion about the need to solve problems related to the municipal level and related to ensuring the ecological, economic and social sustainability of the territory is substantiated.