The paper describes one of the approaches to solving the problem of ensuring the reliability of automated manufacturing system of hazardous chemical plants using various hazardous chemicals in the production processes. Exposure to these substances can be harmful to personnel and infrastructure. Our goal is to create an automated manufacturing system that ensures not only fault-free operation, but also the safety of automated manufacturing systems of hazardous chemical plants. Depending on the type and specifics of the hazardous production, the automated manufacturing system should have a certain integral level of safety. We have developed a method for analyzing system reliability, taking into account many reliability indicators. The proposed method, considering the target probability of failure-free operation of the entire system and the probability of failure-free operation of the hazardous module required for the desired integral level of safety, determines the target probability of failure-free operation of all the system modules. It also provides for the inclusion of not only functional modules into the system, but also modules that block failures and dangerous effects. The paper considers an example of chemical production, however, the proposed method is applicable to a wide range of technological processes of hazardous industries.