A methodology for the modelling and investigation of the safety of complex technical systems is proposed. Complex technical systems are considered to be unique technogenic objects that are designed in one or two instances, implementing extreme technologies, and are subjected to the influence of mechanical, physical and chemical factors. The generalised cause-effect complex and the scenario of violation of the reliability and safety for such systems are formulated. Dynamic models related to the formation of the system states are delineated -from an initial defectiveness of the construction to the damages, destruction, failure, pre-emergency, emergency and possible technogenic catastrophe. A concept of an intelligent program system, which is intended for the computer-aided investigation of reliability and safety, is described. The example for the application of the proposed methodology describes the safety violation of a pipeline under an ammonia synthesis column. The results obtained provide for the efficient and qualitative investigation of revealing hazards and for the delineation of techniques and aids to ensure reliability and safety.