The problem of improving the safety and sustainability of transport in emergency situations holds a special place in the national security of the state. With transport enterprises there are associated state interests such as territorial integrity, the unity of economic space, provision of external economic relations of Russia and its integration into the global economic system. The study showed that in the field of risk management through extremely situations (ES) on the transport it’s situation, when the systematization and deepening of knowledge is extremely difficult without specifying of the conceptual foundations of the theory of risk management and ensure its semantic content in line with the true essence of display of the phenomena of risk management. Moreover, the question of risk management have not been sufficiently formalized and structured risk management model demand development. Here it should be recognized that the study of tools of emergency risk management on the transport, so far not received adequate attention. As a result of the situation, when the existing set of theoretical propositions for risk management of emergency on transport could not determine how to operate effectively in the new environment, and the practice of risk management is largely insufficient. These circumstances caused the act-almost, goal and objectives of the study. The purpose of this study is to develop new, and adapt existing instruments of risk management of emergency transport to improve the efficiency of transport enterprises (TE). To achieve this goal the following tasks were accomplished: 1. The mathematical measure of preventing a terrorist act based on the selection of the most probable places and the method of implementing the attack, as well as establishing a sufficiently adequate model of the intruder, i. e. parameters describing the size, capability and readiness of terrorists. 2. The approach to risk assessment of ТЕ based on the application of the method of data fitting and the method of expert estimations. 3. The proposed use of modern technology, broadening the range of instruments to prevent emergency situations and characterized by the use of: scanning objects; preventive measures; control of objects on the ТЕ; inform on actions in case of emergencies. Theoretical and methodological basis of research is works of domestic and foreign scientists on risk management, regulatory - legal acts of the Russian Federation, methodological developments in the field of management of transport enterprise in the conditions of uncertainty. During the research used the general scientific methods and methods of system analysis, mathematical and statistical methods, sources on the Internet, impact of research of the consulting companies in the field of risk management, the empirical and calculated data, obtained by the author. The theoretical significance of research results is development of theoretical positions on the risk management of emergency situations on transport in the modern conditions. Developed findings expand the theoretical base of this research area and can be used in further scientific developments in the field of risk management. The practical significance of the study is to create tools to improve the effectiveness of risk management of emergency situations on transport. The tools can be used for further scientific studies of, in curricula of universities and training courses management training.