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In recent years maritime logistics infrastructures are the global links among societies and economies. This challenges adversaries to intrude on the cyber-dependent ICTs by performing high-level intelligent techniques. A potential cyber-attack on such infrastructures can cause tremendous damages starting from supply chain service disruption ending up with threatening the whole human welfare. Current risk management policies embed significant limitations in terms of capturing the specific security requirements of ICTs and control/monitoring devices, such as IoT platforms, satellites and time installations, which are primary functioning for the provision of Maritime Logistics and Supply Chain (MLoSC) services. This work presents a novel risk assessment methodology capable of addressing the security particularities and specificities of the complex nature of SCADA infrastructures and Cyber-Physical Systems (CPSs) of the Maritime Logistics Industry. The methodology identifies asset vulnerabilities and threats to estimate the cyber-risks and their cascading effects within the supply chain, introducing a set of subsequent security assessment services. The utilization of these services is demonstrated via a critical, real-life SCADA scenario indicating how they can facilitate supply chain operators in comprehending the threat landscape of their infrastructures and guide them how to adopt optimal mitigation strategies to counter or eliminate their cyber-risks.