Food, energy, and water scarcity increasingly threaten economic stability, social welfare, infrastructure reliability, and long-term national resilience because disruptions across these sectors are deeply interconnected. This study aimed to formulate an integrated framework for optimizing institutional and stakeholder roles in countering Food–Energy–Water scarcity threats and strengthening national resilience. A qualitative case-study design was employed through semi-structured interviews, policy and institutional document analysis, stakeholder-role mapping, Food–Energy–Water nexus assessment, and role-gap analysis. The findings revealed that fragmented governance, overlapping mandates, weak information sharing, and limited cross-sectoral coordination intensified resource vulnerabilities, while clearer role allocation and adaptive coordination improved institutional responsiveness. The analysis identified differentiated functions across prevention, preparedness, response, adaptation, and recovery, with national institutions providing strategic coordination, local authorities supporting implementation, research institutions supplying evidence and innovation, private actors strengthening infrastructure and production capacity, and communities contributing local adaptation and demand management. The study concludes that national resilience depends less on expanding institutional involvement than on aligning authority, capability, responsibility, and coordination across interconnected resource systems. The proposed framework contributes an adaptive governance model for managing cascading scarcity risks through role clarity, capability matching, integrated information, coordinated redundancy, and accountable interinstitutional action under increasingly complex and rapidly changing national resource-security conditions.