Abstract: This study examines the position of sub-districts in the implementation of village government or “Customary Village” in Jayapura District, aiming to analyze the existence of sub-district in performing its duties to coordinate public activities; control, monitor and evaluate the implementation of “Customary Village” governance. The scope of this study includes 4 sub-districts with customary village government: East sentani, Nimboran, Raveni Rara and Kemtuk. It also includes regional work units such as offices and departments. This study used mix-method-sequential explanatory design with the analytical construction of quantitative-qualitative combination that supports the analysis. The result of the study shows that the delegation of authority has been executed, yet it has not been optimum (60.40%). Statistically, it can be generalized that each indicator included in the model has the capacity to reasonably explain exogenous and endogenous latent variables. Based on the empirical strengthening model of sub-district, the reposition of sub-district authority is vital to optimize the implementation of camat’s duties, thus improving the role of sub-district. Accordingly, the impact of power-variable tends to be positive and most-valued of all variables (0.318). This is obtained after adding the sub-district funding, allocated for infrastructural improvement (work equipment) and resuscitating human resources and sub-district institutionalization. To maximize the functions of sub district, its funding, power and camat’s functions need to be strengthened to its fullest, knowing that those three variables retain significant total effect, i.e., 0.423, 0.198 and 0.620, respectively.