This study analyzes policy instruments for conserving hermatypic coral ecosystems in Japan. First, it reviews the regulations for conserving coral reefs in marine protected areas and, second, analyzes the necessary regulations against each type of deterioration factor. As a result, present guidelines are not sufficient for preventing degradation by overuse. To supplement these, the government provides a method that they officially authorize, that is, voluntary rule agreed by local stakeholders under the framework of the Ecotourism Promotion Law. However, the effectiveness of this approach is limited. Moreover, a case study of the Kerama Islands shows strong stakeholder incentive for establishing this rule is necessary for convention creation. Additionally, it is important to design the consensus building framework to save transaction costs.