Although Magoon was working for the Canal project, his office and residence remained in Washington, DC. On March 29, 1905, President Roosevelt unexpectedly called for the simultaneous resignations of all members of the Canal Commission and the governor of the Panama Canal Zone, George Whitefield Davis. According to Secretary of War William Howard Taft, this clean sweep was due to the "inherent clumsiness" of the Commission, especially as related to sanitary problems in the Zone, as well as the difficulty of reaching consensus between the current seven commissioners. Several days later, replacement appointments were announced: Magoon was appointed both governor and a member of the Commission, with railroad entrepreneur Theodore P. Shonts made chairman of the Commission. The new Commission had seven commissioners, as required by the act of Congress that created the body, but responsibilities were to be split such that only Magoon, Shonts, and the chief engineer had any real authority. The remaining four members of the commission were appointed only to fulfil the letter of the law. Congress had already rejected a request by the President to formally make the Commission a three-member body; restructuring the organization was an end-run by the President around that restriction. In order to assume his new duties, Magoon relocated to the Canal Zone the following month. Magoon's primary responsibilities within the Canal Zone were to improve sanitation and to deal with the all-too-common outbreaks of yellow fever and malaria. At first, he refused to believe that the diseases were carried by mosquitos because, he reasoned, the native population would have been more affected. At this time, the nature of human acquired immunity to diseases was not well understood. The "Chicago Tribune", in an article about conditions in the canal, referred to the notion that yellow fever was carried by mosquitos as "bugaboo". However, by January 1906, Magoon had long come to understand the role of mosquitos in the transmission of diseases, as evidenced in a New York Times article wherein Magoon addressed criticisms of his administration in detail; by then he had undertaken a vigorous and ambitious plan to eliminate the swamps that bred mosquitos. While governor, he worked with translators in the War Department to publish an English edition of the complete Civil Code of Panama, which he codified as the law of the Canal Zone on May 9, 1904. This was the first time that the complete civil code of a Spanish-speaking country not a U.S. territory had been translated into English. It was significant that he did not make changes to these laws when "importing" them into the legal system of the territory that he governed.