This study presents the environmental impacts of agricultural policy instruments as evidence from an ex-ante farm-level policy simulation model in Japan. Simulations did indicate that all types of agri-environmental payments achieved the environmental benefit for the land studied. Conversely, market price support does not inevitably increase nitrogen runoff or greenhouse gas emissions at any time since paddy fields themselves have the function of purifying water pollution and work as a biodiversity nursery. The direction and magnitude of the policy impacts are an empirical matter that should be considered carefully at a local level.