In environmental policy in Japan, the benefits derived from agro-ecosystems have traditionally been defined as "multiple functions of agricultural production activities." Even after the concept "ecosystem services" was introduced to Japanese policy, it was not often used for agriculture and forestry where policy mostly evolves around the term "multiple functions." Streamlining the concepts would clarify future policy. This paper aimed to identify future pathways for satoyama as resilient socio-ecological systems based on a review of past and current environmental policy that had an impact on secondary ecosystems in Shiga Prefecture, Japan. From case studies on two diverse satoyama landscapes, natural resource use and the impact of national and prefectural policy were examined. Based on these reviews, two directions to be taken were clarified: the first direction involves the use of grants and other legal support frameworks to ensure that agriculture, forestry, and fisheries industries and the local community conserve and enhance ecosystem services while implementing farmland consolidation and labor-saving measures. The second direction implies efforts to discover and identify values in traditional satoyama structures in areas where the conditions for agricultural activity are relatively unfavorable and unprofitable. The results showed that a better integrated regional policy framework is needed. It should comprise both directions while taking into account the natural and cultural features of each satoyama.