Port risk management (PRM) during port operations is a current problem that can negatively affect the environment, people, and economic issues. In the literature, there is an enormous amount of research related to supply chain risk management (SCRM) in various areas and with various objectives. However, PRM has not received the same degree of attention. In fact, port terminals are crucial links in most supply chain networks and an important pillar of international trade. Therefore, for better risk mitigation efficiency, a risk assessment and prioritization step are vital. Recently in the literature, researchers have applied prospective methods such as structural analysis methods to risk prioritization in SCRM. The aim of this research is to prioritize various man-made risk variables in PRM using a qualitative structural modeling-based approach, specifically, the MICMAC method (referring to its French acronym: Matrice d’Impacts Croisés Multiplication Appliquée à un Classement). An empirical study was conducted to assesses and prioritize risk variables of the seaport terminals of Sfax (Tunisia). The main contributions of the empirical research are twofold. First, to prioritize the key risk variables to define the most critical ones that require immediate intervention. Second, to analyze the structure of the influences between all identified risk variables. The results for the port terminals of Sfax show that the highest-priority risk variables are the manual handling (Ph3), disregard for safety aspects (Ph4), unsafe storage of goods (Inc1), absence of a prevention system and a rescue organization (Inc2), neglect of the regulatory aspects of handling equipment (M1), ignorance of good handling practices during the operation of loading and unloading (Cho2), and inadequate lifting accessories (Cho3). These risk variables must be the subject of urgent risk reduction strategies.