The purpose of the study is to identify industrial facilities that are critically important for the fuel and energy complex in the conditions of joint functioning of industries, taking into account the system effect and existing mechanisms of structural redundancy. To identify critically important facilities of the fuel and energy complex based on its operation models derived as a result of stage-by-stage sectoral and general energy studies, a methodology is proposed. It is based on the identification methods of critically important industry facilities on the principles of assessing vulnerability of critically important infrastructure elements. The presented methodology is characterized by the complex and flexible assessment of the critical importance of sectoral facilities, which is carried out on the basis of scenario options of fuel and ener gyomplex operation. The methodology is supplemented with a formalized representation of a typical general energy optimization model, which unifies the relationship between the territorial-production structure of the sectoral systems modeled in it, its information base with the corresponding technical and economic indicators, and the research problems solved with its help. The assessment of the critical importance of gas industry facilities is given for 80 constituent entities of the Russian Federation. The approbation results of the proposed methodology are given on the example of the identification of the critically important gas industry facilities using a model of fuel and energy complex operation with a detailed scheme of the Unified Gas Supply System of Russia. The approbation has revealed the differences in the priority of critically important facilities of the gas industry and the fuel and energy complex. It has also shown a significant influence of the system effect of the mutually coordinated functioning of industries on the fuel and energy supply of consumers. The results obtained confirm the efficiency of the methodology, prove the possibility of its use for assessing the critical importance of power industry branch facilities. The research scheme implemented in the methodology allows to obtain an adequate state of matters with the fuel and energy supply to consumers under cut-out critically important sectoral facilities.