Due to an increasing demand of energy from renewable resources, wind energy is of high demand, especially in areas that have constant high wind intensity. Indonesia is considered an archipelago, where there are many areas that are suitable for building wind farms. However, there are different factors that may affect the site selection for a wind farm. In this study, we propose a hierarchical dual data envelopment analysis (DDEA) model that can be used to identify the suitable location for building a wind farm. Important factors related to geographical and structural technicality are considered in the analysis. Locations from each region of Indonesia were selected at both district and provincial levels. Districts and provinces are considered for decision-making units (DMUs) which are evaluated for efficiency scores based on the DDEA method. The DDEA method is a multi-criterion and non-parametric estimation method that can be used to measure DMU performances. The proposed hierarchy consists of two levels, which are defined based on 165 districts and 33 provinces in Indonesia. The results show that South Sumatra province has the highest potential for construction of wind farms, especially in the district of Palembang. West Papua, Papua, and Maluku provinces have descending priority based on good infrastructure accessibility, high wind velocity, and are less prone to natural disaster.