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The importance of communication, information sharing and interoperability in an emergency response scenario have risen recently based on the frequency of disasters throughout the world and the wide range of severities and degrees of impacts. This work contributes to the area of emergency response communication qualitatively by presenting a systematic approach to develop an organizational communication model to improve overall emergency response. Establishing and accessing a reliable communication infrastructure at crisis is crucial in order to have accurate and real-time exchange of information. This work identifies a set of potential network oriented problems in existing inter-organizational communication protocols incorporating the information collected at several drill participations and interviewing the first responders. We conquer the complexity of a large, unique and unpredictable emergency response process by a top-down approach. We are constructing a high-level hierarchical Petri net consisting of decoupled individual organizations gathered at a crisis site to model the interactions among different jurisdictions. This abstracts each organization as a sub-block in the overall model which provides flexibility in study at a high-level while does not involve with the details. We present organizational challenges on communication technology and inter-organizational communication protocols identified during the drill.