The main problems and possibilities of emergency management in complex logistics systems are considered. A hierarchy of models of complex logistics systems is presented, including an extended transport model, a model for accounting for uncertainty, a scenario model of functioning and development. The hierarchy of situations that may arise from the point of view of a decision-maker in the process of functioning and development of controlled objects has been determined. The concept of an emergency situation is given, the sources of their occurrence in complex logistics systems are indicated. A methodology for conducting a situational analysis based on the study of scenarios of behavior of various components of a complex logistics system is proposed. A work program for scenario research of emergencies in complex logistics systems is proposed