The need to increase the capacity of ports is due to the development of the Northern Sea Route as a national transport route of Russia in the Arctic, the National Program for the Development of the Far East, in the context of an increase in trade with other regions of Russia, as well as the reorientation of cargo flows from the Baltic ports to Russian ones in Primorsk, Ust-Luga and Vysotske. Increasing cargo turnover and ensuring the strategic economic interests of Russia requires the reconstruction of existing and construction of new modern port-industrial complexes, provided with advanced technologies, including the automation of logistics management processes, production and engineering systems. This article describes a method for mathematical modeling of the failure of control systems for automation of cargo terminals of ports. Since failures in the operation of automation systems lead to an increase in the load of cargo berths (terminals) of both sea and river port complexes, to a violation of logistics schemes, and as a consequence to an increase in costs. Modeling is carried out using methods of probability theory, in particular, the Poisson distribution law. A comparison of the empirical and theoretical failure rates of automation is performed using the Pearson criterion. The performed modeling will allow determining the technical and economic indicators of new construction, reconstruction or overhaul, in terms of the engineering systems of the facility, and optimize the automation processes.