Port logistics information system was deemed as core competence of port logistic functions. Its main components include navigation assistance system, handling and delivery system, warehousing system, inland access system etc. our government has sponsored various port logistic systems programs including Port-MIS, Port-EDI and MTNet under the guideline of Asia Pacific Operating Center projects. Nevertheless, it still existed a number of problems need to resolve, such as inefficient information infrastructure, higher transit expense, bad transit efficiency and quality, off-line between government authorities, expensive hardware and software setup cost of EDI system, various information system between private shipping and port related users and so on. The purpose of this paper is aimed to identify the issues of Taiwanese port logistic systems, and to discover the alternatives based on comparative analysis approaches among International ports in Asia Pacific Area.