The governance of marine conservation in Indonesia has been the subject of critique for decades. This paper elucidates and analyses the legal framework for marine mammal protection and current institutional arrangements, and reveals gaps and overlaps in the national legal and policy frameworks for marine mammal governance in the Archipelago. We reviewed available policies to assess the current regulation practices in the country's marine mammal protection. In total, five relevant international conventions, 28 Indonesian national regulations, and 16 provincial regulations on marine spatial planning were found. Progress on legal framework regarding marine mammal governance reveals three different phases: 1970s (species-centred approach), 1990s (site-based approach), and current (wider marine management approach). We summarized seven policies based on the following characteristics: species, site and other values. We identified functional overlap and unclear mandates as the main shortcomings of these regulations. Although marine mammal protection in Indonesia enjoys a set of regulations, the practical actions required by these regulations are still unclear. Protection gaps still exist, rendering conservation efforts less effective. The paper argues how an adequate and appropriate legal framework and institutional arrangements will ameliorate and strengthen marine mammal governance in Indonesia. We suggest some urgent-yet-lacking policies that should be added to the current regulations, including regulations on traditional whale hunting, the code of conduct for marine mammal watching tourism, standards for aquaria, and the legal basis for marine mammal stranding network and underwater noise pollution. We endorse the cetacean National Plan of Action for it is designed to enhance ecological and human-dimension research on cetaceans and address the detrimental effects of anthropogenic activities to the cetaceans. We suggest establishing a mechanism for cross-institutional coordination for more effective marine mammal protection in Indonesia. Becoming a full member of the Convention on the Conservation of Migratory Species of Wild Animals and International Whaling Commission will further strengthen the conservation management of marine mammals in Indonesia.