Indonesia, as an archipelagic country, has an uneven population distribution and limited economic activity. Regarding this fact, sea transportation has a significant role in improving welfare, especially for those who live in particular areas, which are in Indonesia called 3TP areas (remote, outermost, and border areas). To spur the development of the 3TP areas, the government has implemented a policy of providing subsidized shipping (non-commercial shipping), which is called “Perintis” shipping. This service connects remote areas in order to improve accessibility. Subsidized shipping has the characteristic of ‘Transport Promote the Trade,’ so it cannot be judged as profit-oriented commercial transportation in determining its success. The aim of this paper is to assess the benefits of subsidized shipping based on economic factors and social welfare. This research is conducted in a case study of the Tanimbar Islands district, which is a district that is included in all the criteria for the 3TP area, and using the analytical hierarchy process method. The results show that the Tanimbar islands district is included in the category of underdeveloped and outer/border region, which has the percentage of each criterion as follows: politics is 26%, economics is 14%, social-cultural is 8%, and security and defense is 52%. From the results of the benefit calculation, the Tanimbar Islands district is a region with a high benefit value, namely 0.0188.