Abstract: The continuous development of automated control systems for industrial facilities leads to the emergence of more advanced and complex control algorithms. A natural consequence of the development of control systems (CS) is the use of more complex technical means: sensors, controllers, SCADA and MES systems. Ultimately, the saturation of systems with additional software and hardware leads to a decrease in manageability in general, since software needs to be updated, equipment often fails, needs replacement, etc. Thus, approaches aimed at creating separate, autonomously functioning subsystems are becoming a thing of the past. An integrated, multi-level joint management of the entire infrastructure of the process control system is needed, from the technological facility to the technical infrastructure, which is closely tied to the facility. The article discusses the issues of constructing top-level control subsystems for the process control system, when it is necessary to control directly the software and hardware as part of the process control system. As research methods, simulation and computer modeling was used, which made it possible to evaluate the effectiveness of the proposed approaches and management methods. Also, the research results were verified through the pilot implementation of an automated incident management system based on the proposed approaches in the process of managing a complex technologically object. The novelty of the research lies in the proposed approach to incident management in automated process control systems, which makes it possible to improve the quality of management, reduce management costs, and predict (in some cases) the occurrence of new incidents and take measures to prevent them. Studies have shown the feasibility of using the proposed approach to control complex non-stationary automation systems.