This study aims to analyze the implementation of development policies in border areas with the lens of the role of central and regional governments in its implementation. By using qualitative methods, the data sources come from observations, interviews and documentation on policy frameworks and constraints makes it possible to strengthen the environmental aspect as a configuration background for designing policies aligned with sustainable development. The results show that the current border area development policy uses three approaches: security, welfare, and the environment. On the other hand, there is a gap between the regional autonomy policy's contents and the central government's policies. Thus, the Jayapura city government's role is limited to implementing border area development. This finding is an important reference for aligning the visions of the central government and local governments in sustainable development in the periphery.