With the increase in disasters due to climate change, there has been a growing interest in green infrastructures that utilize nature for disaster risk reduction (DRR). However, green infrastructures cannot completely protect against hazards. Therefore, this study investigates the public preference in Japan for DRR and its uncertainty using a survey-based choice experiment. The results showed that benefits were obtained from the increase in “success probability”, “reduction in human damage”, “reduction in property damage”, and “reduction in indirect damage”; however, the benefits obtained from additional improvements diminished. Moreover, the results of our analyses revealed that preferences for DRR and its uncertainty were heterogeneous among respondents, and the population segment that includes more women, older people, and more people who live in areas that may be directly affected by floods had higher ratings for “success probability” and relatively slightly lower ratings for “reduction in indirect damage”.