Since the Nationalist Party lost the Chinese Civil War and moved to Taiwan in 1949, the criminal procedure and prosecutorial system for the most part has remained unchanged. However, because the Ministry of Judicial Administration, which was a branch of Executive Yuan, was charged with the appointment and supervision of high courts and district courts, many people contended that the executive power of the government invaded the judicial area. Finally in 1980, the Law of Court Organization was revised and all high courts and district courts were transferred to Judicial Yuan. All prosecutors offices and prisons remained in the Ministry, which was still a branch of Executive Yuan. This structure continues today.
       When Taiwan was returned to Chinese rule in 1945, the litigation cases in Penghu County were still under the jurisdiction of Kaohsiung District Court. Therefore, all litigation parties and witnesses in Penghu County had to go to Kaohsiung by ship over Taiwan Strait. The Ministry of Judicial Administration, which was renamed as the Ministry of Justice, permitted the foundation of the Penghu District Court and the Penghu District Prosecutors Office on December 26, 1949. 
       As the caseloads and numbers of the personnels increased, the offices had been widened twice in 1975 and 1982. To further improve the office environment and the quality of our services, the Judicial Yuan and the Ministry of Justice held bilateral conference and reached an agreement to construct a new office building adjacent to the south of the Penghu District Court Magong Summary Court. The Penghu District Prosecutors Office accordingly drew up a construction plan. The new office starts functioning on March 26, 2007.