<p>Objective　To describe the structure and efforts of the health sectors in municipalities to address the COVID-19 pandemic from the first infected case to the second wave.</p><p>Method　We conducted self-administered postal questionnaires with the department head or an equivalent position of the 1,741 municipal health departments (108 cities or districts with public health centers (PHC) and 1,633 general municipalities) in Japan as of November 1, 2020. The survey period was from November 11, 2020 to January 8, 2021. The respondents were asked to provide the type of local government they were affiliated with, the number of COVID-19 cases in their municipality between January 16 to November 1, 2020, the operational structure of the health sectors after the pandemic began, and efforts made to address it. The analysis tested for the differences in response rates by cities with PHC and general municipalities, and by population size of the general municipalities.</p><p>Results　A total of 1,270 valid questionnaires (valid response rate 72.9%) were returned from 83 cities with PHC and 1,187 general municipalities. Concerning the operational structure, over 90% of the cities with PHC transferred personnel from other departments to the department of infection control. Over 80% of all municipalities found a way to hold meetings remotely. More than half of the cities with PHC centers had employees working from home. Fewer than 50% of the general municipalities had a business continuity plan (BCP) prepared and in place for an outbreak, such as a novel influenza. Concerning the efforts within the local government, high rates of “secured supplementary budgets” and “monitored and secured infection control equipment” were reported. Concerning the efforts directed toward related organizations, over 70% of the cities with PHC “supported contact tracing at the PHC” and “monitored the stock of infection control equipment and procured equipment to address the shortages at medical institutions, welfare facilities, etc.” Meanwhile, approximately 80.5% of general municipalities “corresponded and coordinated with medical institutions concerning the health examinations and services, etc.” Concerning the efforts directed toward the public, over 90% of the respondents, regardless of local government type, “wrote articles and disseminated information regarding the infections in public relations (PR) reports or online” and “responded to inquiries from the public.” In general municipalities, the larger the population size, the higher the percentage of implementation.</p><p>Conclusion　Although the municipalities responded to the transmission of the COVID-19, there were some issues. Further preparation for the pandemic is required.</p>