In modern conditions, the relevance of the problem of assessing the information security risks for automated systems is increasing. Risk assessment is defined as a complex multi-stage task. Risk assessment requires prompt decision-making for effective information protection. To solve this problem, a method for automating risk assessment based on fuzzy cognitive maps is proposed. A fuzzy cognitive map is a model that can be represented as a directed graph in which concepts and connections between them have own weights. The automation process allows evaluate complex relationships between factors and threats, providing a more comprehensive risk assessment. The application of fuzzy cognitive maps proved to be an effective tool for automation, promptness, and quality in risk assessment.