Coordination in humanitarian operations has always been challenging due to the uncertainty and the complexity of the operations. Because no one collaboration strategy fits all, the exploration of coordination mechanisms for a particular context is therefore necessary. The present paper aims at investigating the coordination mechanism among the key players and identifying challenges of coordination in relief operations by governmental regional disaster management agency (Badan Penanggulangan Bencana Daerah – BPBD) in Yogyakarta province, Indonesia. Qualitative research using semi-structured interviews focusing on coordination mechanism during the preparedness and response phases of humanitarian operations was conducted with representatives from provincial BPBD of Yogyakarta. The findings entail that the hybrid coordination approach, characterized by a centralized structure combined with vertical and horizontal collaboration to ensure smooth aid procurement and distribution, has been implemented. The BPBD serves as a director that leads and coordinates the humanitarian operations with other involved stakeholders including other governmental services, local and international non-governmental organizations, and local and regional communities. The collaborations are engaged at the strategic, tactical, and operational levels. The findings have indicated that cultural and knowledge barriers (different thoughts and perceptions), ego-sectoral, political issues, limited technology for sharing information (mostly using social media), and trust, were the main reported barriers toward coordination in humanitarian operations. Avenues for potential future research are also discussed.