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This study examines how the Swedish Armed Forces Command and control structure at the strategic level aligns with the collaboration requirements formulated within Sweden’s total defense system, particularly by the Swedish Civil Contingencies Agency. The study addresses a research gap, where previous studies have primarily focused on social and cultural aspects of civil vs military cooperation, while the structural dimension of military leadership has received limited attention. The analysis is based on a qualitative text analysis of official doctrines and policy documents from both military and civilian perspectives. Max Weber’s theory of rationality, as developed by Karlberg, is applied as an analytical framework to examine differences in organizational logic. The findings indicate that there is a high degree of alignment at a conceptual level, as both actors emphasize flexibility, responsibility and situational awareness. However, significant differences emerge in practical application. The armed forces rely on a hierarchical structure design for efficiency and control, meanwhile civilian actors emphasize network-based coordination and decentralized decision-making.  The study concludes that while the system is compatible in principle, structural differences may create challenges for effective collaboration in practice.