All previous ministers have been held over except for the ministers of defense and justice; the chairmen of the Mainland Affairs Council (MAC), Veterans Affairs Commission (VAC), and the Public Construction Commission (which is not a cabinet-level agency but whose chairman must be concurrently a minister without portfolio); the cabinet secretary-general; and one minister without portfolio.
行政院內閣改組人事案於民國八十八年一月二十七日在國民黨中常會通過，計有國防部長、法務部長、陸委會主委、退輔會主委、公共工程委員會主委及行政院秘書長、一席政務委員異動，其餘皆留任。