Objective Ota City, located in southeastern Tokyo, including Haneda Tokyo International Airport, has numerous scattered lodging facilities. Shortly after the first case of SARS-CoV-2 B.1.1.529 (Omicron) variant was reported abroad, the Japanese government strengthened border control measures, including quarantine procedures and public health official involvement, for incoming travelers. This study aims to propose effective and efficient border control measures to prevent future outbreaks of emerging and re-emerging infectious diseases.Methods Border control measures implemented between November 2021 and mid-January 2022 were analyzed from three perspectives: chronological changes in government notifications, the situation of in-flight contacts and Omicron cases, and the support system for coronavirus-disease 2019 control department of the Ota City Public Health Center. Additionally, a questionnaire survey was conducted among public health centers with jurisdiction over the top four international airports. This survey aimed to assess the effectiveness of the support system, evaluate cooperation with related organizations, identify common issues faced by public health concerns, and gather suggestions for improvements in future border control measures.Results The definition and treatment of in-flight contacts of Omicron-positive individuals were initially outlined on November 30, 2021, and underwent frequent revisions until January 14, 2022. Between December 1, 2021, and January 12, 2022, only one Omicron case was identified among the 470 tests conducted on in-flight contacts. However, out of 136 additional domestic specimens collected (including 57 positives for genetic analysis), 40 were confirmed Omicron positive. The results of the questionnaire survey across the four public health centers largely mirrored the issues and suggestions identified by Ota City officials. A significant portion of these issues arose from managing temporary non-Japanese residents staying near international airports.Conclusion Border control measures should be implemented to delay the domestic spread of the virus. In this reason, it is crucial to avoid placing an undue burden on public health officials responsible for handling domestic infections. Since response policies and target definitions may need to adapt to unknown pathogens, they may be changed frequently, baffling the officials; however, a system for collecting real-time data from frontline sites and making evidence-based decisions is essential. Additionally, deploying liaisons from national and prefectural governments to focal points of emergency response would strengthen the support system by promoting unified instructions and information sharing.