In this paper the general fundamentals of the formation of the balance of fuel and energy resources were determined and the main components of the general energy balance were substantiated. It was formed according to the indicators from the state energy statistics of Ukraine, and on the basis of the obtained data the analysis of energy flows was carried out. Mathematical substantiation of its support on the traffic of energy flows from their extraction (production), transformation and final consumption was offered. The algorithm for compiling the overall energy balance was detailed to eliminate possible discrepancies between the indicators during the final operations of the balance sections. In order to ensure timely response to unsolved problems in the energy sector of Ukraine, it is proposed to implement a constant monitoring of the energy balance as a whole and by partial indicators. The use of a new algorithm for optimizing the balance of fuel and energy resources (FER) for individual balance sheet items was proposed. A model of organizational and economic mechanism was developed to study the functional interactions of international organizations in the field of energy independence, administrative and financial institutions, fuel and energy entities and the national economy, which are subjects of all hierarchical levels of energy security. It reflects the equivalence of two main aspects of energy security of the national economy: ensuring the stability and efficiency of the fuel and energy complex on one hand, and the formation of energy efficient consumers through the introduction of innovations and energy saving technologies, on the other.