The management of emergencies affecting interdependent critical infrastructure (CI) systems is a complex issue of increasing concern. The existence of multiple cascading effects, limited situational awareness, and the need for coordination between several actors are factors that justify the conceptualization of CI as a complex adaptive system (CAS). Although the capability concept has been extensively adopted in emergency management (EM) literature, proper classification and modeling of CI systems is lacking. This study aims to adopt a capability-based approach for EM to improve the adaptability to the prevailing and unpredictable circumstances, based on a combination of literature review and field research. It proposes a classification and modeling framework for the analysis of the intra-and interorganizational capabilities using a pilot application involving the Italy-Switzerland cross-border transport infrastructure. This framework is suitable for modeling the EM capabilities under different operational contexts and emergency scenarios. Moreover, it enables the representation and description of a CI system through elementary components that capture the main features of a CAS. The obtained results indicate that the proposed framework can foster public-private collaboration (PPC) in the development of CI protection and resilience (CIP-R) programs.