The chapter describes the results of studies aimed at the effective functioning of the computer system for managing information security risks of the automated process control system. At the same time, the limitations on the cost of applied protective measures using risk-oriented methods are considered. For this purpose, it is possible to use genetic algorithms: classical and compact. The results of the study are appropriate to use when building information security systems for the automated process control system. To perform the work, the methods of the metaheuristic approach were used to find the optimal configuration of protective measures for the multi-level architecture of the automated process control system. An algorithm is proposed for determining the optimal set of protective measures based on the analysis of information security risks using the metaheuristic method. The main functions of the genetic algorithm used are described. The operation of the proposed algorithm is demonstrated using the example of determining the protection configuration for a typical gas producing enterprise.