The article discusses the issues of evaluating the effectiveness of the system of physical protection of critical facilities and the development of control solutions to ensure the necessary requirements for it. The relevance of the presented tasks is due to the increase in the number and types of violations, the improvement of the technical capabilities of violators, the complexity and variety of objects of protection. The presented methodology for making effective management decisions to ensure the physical security of critical facilities is a comprehensive study of physical protection systems. With the help of a simulation model, the probability of a safe state of the object on the specified routes of penetration of the intruder is estimated. The method of principal components revealed latent connections between routes, on the basis of which the decomposition of the complex task of managing the physical security of the object was carried out to obtain more reliable dependences of the probability of the safe state of the object on the parameters (characteristics and structure) physical protection systems. For each group of routes the probability of a safe state of the object of which is insufficient, a regression equation is constructed using a complete factorial experiment – a unique function of the object’s safety management. The analysis of the coefficients of the regression equations makes it possible to make effective management decisions to modernize the structure of the physical protection system, increasing its effectiveness to the required value.Obtaining management functions is the author’s methodology for making effective management decisions to ensure the physical security of critical facilities and determines the scientific novelty of the work.