While the epidemiological impact of the coronavirus disease 2019 (COVID-19) pandemic has been relatively moderate in East-Asian countries, the pandemic has significantly impacted on citizens’ lives and livelihoods, and Japan is no exception. In the early phase of the COVID-19 pandemic, Japan managed unprecedented quarantines and realized the difficulty of controlling COVID-19, finally recording a relatively high number of deaths per million in the Western Pacific region. However, scant research has highlighted the distinctive features of Japan’s reaction and the challenges encountered. To clarify these points and examine Japan’s first response to COVID-19, we performed a content analysis. Minutes of expert meetings were analyzed from multiple viewpoints, including epidemiology, health systems, border control, and health communication. The obscure evolution of the testing strategy, the usefulness of retrospective contact tracing, the rapid scientific risk assessment, a sluggish expansion of health system capacity and response in border control, and misunderstanding between risk communication and crisis communication are made evident by our analysis. Examining previous responses and gathering lessons learned in each country will improve global responses to COVID-19 and strengthen regional health security. Therefore, while investing in public health and ensuring transparency, Japan needs to clarify the previous decision-making process of each countermeasure towards COVID-19.