The article focuses on the issues related to the building and functioning of the system of  protection of  population and territories from natural and man-made emergencies in Russia in the context of modern challenges and threats. On the one hand, the established state system of protection, which has a multi-level and complex character, allows effective responding to emergency situations. At the same time it should be noted that its performance generates increasing dysfunctions associated with inadequate orientation at the tasks on monitoring and forecasting of emergency situations, the continuing fragmentation of its individual elements and unclear distribution of powers in the spheres of protection from emergency situations and civil defense. The hypothesis of  the authors of  the article is  that the existing division of  spheres of  management, on  the one hand  – by  the protection from emergency situations, on the other hand – by civil defense, is of largely artificial manner and therefore resulted in a doubling of organizational structures and policy management. The analysis of law enforcement practice, as well as historical development and the international experience of  regulation, affirms the need for a  considerable adjustment of the institutional basis for the functioning of various elements constituting the unified state system of prevention and liquidation of emergency situations and the civil defense system. The authors substantiate that the priority direction of the development of  public administration in  this sphere should be  the creation of  the civil protection system as a holistic object of state regulation combining both protection from emergency situations and civil defense.