The relevance of the problem of physical protection of ports along the Northern Sea Route is noted, where berths for vessels with nuclear power installations are located. The specifics of implementing the physical protection function for such facilities using automated physical protection complexes (PPC) are considered. The vulnerabilities of information in the end devices of such automated systems to threats from electromagnetic interference (EMI) on their hardware base are substantiated. The functional model of the objective function ‘Violation of the security regime of a seaport through EMI on its PPC’ is analyzed as a tool for formalizing such threats, with the aim of constructing analytical models to assess the time characteristics of the implementation of individual stages of this objective function and the objective function as a whole. Corresponding expressions relevant to these models are provided. The developed methodological framework allows for a quantitative assessment of the intruder's capabilities using EMI on PPC with the aim of creating conditions for penetration into the protected area. By correlating the obtained assessments with the capabilities for implementing countermeasures against such threats, it is possible to develop mathematical models of the effectiveness characteristics of these measures. In turn, based on such models, there is an opportunity for a scientific justification of the requirements for the methods and means for physical protecting the Arctic zone seaports.