Tropical peatland degradation due to oil palm plantation development has reduced peat's ability to naturally regulate floods. In turn, more severe and frequent flooding on peatlands could seriously impair plantation productivity. Understanding the roles of peatland ecosystems in regulating floods has become essential given the continued pressure on land resources, especially in Southeast Asia. However, the limited knowledge on this topic has resulted in the oversimplifications of the relationships between floods, commercial plantations and peatland sustainability, creating major disagreement among policymakers at different levels in governments, companies, NGOs and society. Hence, this study identifies whether flood policies are integrated within peatland management through a qualitative policy analysis of publicly available papers, government reports, and other official documents that discuss flooding, and/or more in general, hydrology in peatlands. Document analysis was then triangulated with data obtained from several semi-structured discussions. The analysis indicates that the industry on peatlands and the peatland's environmental sustainability could be threatened by increased flooding. We show that, in spite of this, flood policies in SE Asian countries like Malaysia and Indonesia have not been well-integrated into peatland management. We also discuss how the countries could move forward to overcome this problem.