Objectives: The objective of this study was to elucidate the condition of malaria epidemics during the postwar Occupation period in Japan. Methods: The statistical records listed in the appendices of the “Weekly Bulletin”, an official document of the General Headquarters, Supreme Commander for the Allied Powers (GHQ/SCAP) that is currently kept in the National Diet Library Modern Japanese Political History Materials Room, were converted into electronic files. On the basis of these records, the monthly prevalence of malaria was plotted in graphs to analyze the course of epidemics with respect to time and place. Results: The prevalence was high in all regions in the summer of 1946, when the present records were initiated. As a general trend, the prevalence was high in western Japan and low in eastern Japan. In all regions except the Kinki region, the prevalence decreased with time thereafter and virtually no epidemics occurred after 1948. In the Kinki region, epidemics with a prevalence of over 70 cases per 100,000 individuals repeatedly occurred until 1949, but the prevalence rapidly decreased in 1950. By prefecture, Saga Prefecture showed the highest prevalence in the nation in July 1946. While the prevalence in most prefectures decreased with time, Shiga Prefecture was the only prefecture with recurring epidemics with a prevalence of over 800 cases per 100,000 individuals until 1949. Conclusions: Malaria epidemics during the Occupation were classified into epidemics caused by “imported malaria”, which was observed in many prefectures, and those caused by “indigenous malaria”, which was observed only in Shiga Prefecture.