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Aim: The paper proposes a novel risk assessment method ology for complex cyber-physical systems: The proposed method ology may assist risk assessors to: (a) assess the risks deriving from cyber and physical interactions among cyber-physical components; and (b) prioritize the control selection process for mitigating these risks. Methods: To achieve this, we combine and modify appropriately two recent risk assessment method ologies targeted to cyber physical systems and interactions, as underlying building blocks. By applying the existing method ology, we enable the utilization of well-known software vulnerability taxonomies, to extract vulnerability and impact submetrics for all the interactions among the system components. These metrics are then fed to the risk analysis phase in order to assess the overall cyber-physical risks and to prioritize the list of potential mitigation controls. Results: To validate the applicability and efficiency of the proposed method ology, we apply it in a realistic scenario involving supply chain tracking systems. Conclusion: Our results show that the proposed method ology can be effectively applied to capture the risks deriving from cyber and physical interactions among system components in realistic application scenarios, while for large scale networks further testing should be carried out.