本研究嘗試探討2000年政黨輪替後，民進黨政府在設置中央選舉委員會、國家通訊傳播委員會、金融監督管理委員會等獨立機關時面臨的困境。雖然設置獨立機關有降低政治交易成本、買政治保險及適應社會新式技術等正面效益；然而，這些機關的獨立過程，卻因民進黨與國民黨的政治競爭而屢受挫折，兩大黨都不願意落實機關的獨立性及賦予實權。此政治競爭的場域主要體現在機關的人事權與業務權上：民進黨分別以控制機關的人事任命權及限縮其業務職掌為競爭策略；國民黨則試圖透過修訂機關組織法及爭取人事同意權來掌握這些機關。最終，有的機關失去了獨立性（如金融監督管理委員會）；有的機關雖然獲得獨立，但過程爭議不斷（如國家通訊傳播委員會）；中央選舉委員會則遲至2009年二次政黨輪替後，才在同時掌握行政權與立法權的國民黨政府下成為獨立機關。在此歷程中，獨立機關的人事權一直沒有出現完整而穩定的方案，其制定、執行政策及訴願權等獨立職權也逐步被行政院收回，最後僅剩審理個案的功能。隨著機關獨立性的不斷限縮，民進黨政府原初政治改造的理念不僅失敗，設置獨立機關可能帶來的正面效益也同時衰微了。

This paper explores the difficulties when the DDP government attempted to es-tablish the Central Election Commission (CEC), the National Communications Commission (NCC), the Financial Supervisory Commission (FSC) and other “independent agencies” after the first party turnover in 2000. Although the establishment of independent agencies may have positive effects, such as transaction costs reduction, political insurance, and adaption of new technologies; however, because of the bipartisan competition between the DPP and the KMT, the two major parties are both not willing to implement their independence and authorize power to them. This competition is mainly reflected in personnel and discretion. The DPP controlled the appointment authority and shrink the agencies’ discretion power. The KMT were trying to amend the constitution of these organs. Eventually, some agencies have lost independence (e.g. FSC); some agencies gained independence but controversial (e.g. NCC); and the CEC was delayed until the second party turnover in 2009. In this process, the independent agency’s powers to implement policies and personnel were shrinking. The DPP government’s original idea of independent agencies was failed.