The relevance of the research is caused by the need to form a high-quality concept of a system for management and forecasting of the socio-economic development of the sectoral and inter-sectoral complex of a region. The subject of the research is the methods for forecasting the economic security under conditions of uncertainty. The purpose of the research was to consider and evaluate a model of dynamic integration of economic security for a regional inter-sectoral complex under uncertainty conditions based on the institutional approach principles. The paper analyzes the vectors of structural changes in the regional inter-sectoral complex that includes the mining, manufacturing and construction industries. A methodology for predicting the impact of the digital economy on the economic security of the regional inter-sectoral complex is considered. A new model of forecasting the economic security of the above-mentioned complex was built to be used as a tool for regulating the socio-economic development at the regional level. A set of key conditions for the development of an institutional mechanism to ensure the economic security of the region in terms of its sustainable operation and withstanding internal and external threats and risks were formed. In turn, the institutional concept of the economic security mechanism involves constant selection, analysis and evaluation of judgments about the economic security of a region, country or economic entity. This task is achieved by comparing the numerous characteristics of economic activity. The paper concludes that the proposed method of forecasting using econometric models makes it possible to assess the economic security of a regional inter-sectoral complex and timely respond to negative performance indicators.