Japan is highly exposed to natural hazards, and agricultural producers in Japan have significant experience in managing the risk of natural hazard-induced disasters (NHID). However, recent large-scale typhoons and heavy rain events have highlighted the importance of increasing the sector’s resilience to NHID. A number of current practices build resilience. Disaster risk governance and agricultural policy frameworks are flexible and responsive to evolving NHID risks. Non-structural measures such as hazard maps are increasingly seen as complementary to infrastructure in preventing and mitigating flood risks. Innovative on-farm solutions for mitigating flood risks, such as the paddy field dam, are also increasingly used. Disaster response is rapid, and disaster assistance prioritises helping producers to resume farming. However, agricultural disaster risk management (DRM) must reflect the challenge of more frequent and intense typhoons and heavy rains in the context of ageing and depopulation in rural areas. Public DRM measures should also be complemented by greater efforts from farmers and other stakeholders, such as agricultural co-operatives, to build agricultural resilience to NHID.