There have been serious conflicts related to the port name and jurisdiction on Busan New Port between Busan Metropolitan City and Keongsannam Do. Such conflicts can hamper the competitiveness of Busan Port aiming at achieving the position of logistics hub in Northeast Asia. Therefore this study aims at reviewing the problems caused by the two local governments conflicts at the stance of port users such as terminal operators and logistics centers, and suggesting some measures to solve the problems. For these current literature was reviewed, the difficulties faced by users derived, and some key measures such as Single Window System were suggested.