Since 1996, the document exchange method by EDI has been introduced in port and logistics industries to enhance the declaration activities to the Pusan Port Authority and Customs. In spite of these efforts, users such as shipping companies, shipping agents, and freight forwarders have complained the inconvenience of using EDI systems. The major reasons can be summarized as too much transfer time, inconvenient EDI software, and problems on message receiving confirmation. To solve these problems, although we have developed an Internet based EDI system for Port-MIS users, we have failed its implementation practically for the short of Governments readiness, the complexity of systems and separation with in-house systems. So, the writers have changed the direction of research to applying the concept of SCM to logistics system by XML/EDI. In this Paper, the prototype systems to integrate processes of shipping company, Port Authority, Customs and stevedoring company will be suggested. The new method of EDI gives us advantages, which are the accuracy of cargo data and integration of processes among firms and keeping the service of cargo trace.