Currently, Indonesia’s logistics system has not been maximized, as evidenced by the high cost of logistics that account for about 23.5% of GDP nationally and still far from developed countries that are only 10% of GDP even less. This paper evaluates the performance of logistics systems in Indonesia based on government policy. The cost component that is a problem in Indonesia’s logistics system will be mentioned in this paper based on journals, reports and related regulations. The data is taken by distributing questionnaires to the logistics delivery service providers. The data that has been obtained is analyzed using matrix paired comparison. This method is applied to rank the cost components presented. The result was that the logistics cost component that most affects the cost of logistics in Indonesia are the cost of sea and land transportation, due to too much tax and levy that needs to be spent and inadequate infrastructure.