The public administrative organizations in Taiwan are positively transformed into Non-Departmental Public Body (NDPB) to meet the challenge of globalization and competitiveness. And that is the most important change in the history of Taiwan. Japan has established NDPB positively from 2001, and has set up 107 ones by July 2004. It is so similar in oriental cultural background, state situation and changing timing between Japan and Taiwan that the establishment experience of NDPB in Japan is highly valuable for that of Taiwan. Therefore, this text compares and analyses the establishment of NDPB between Japan and Taiwan, and proposes the obstacles and coping strategies during the process of establishment of NDPB in Taiwan to guide the future directions.