Japan Customs introduced the Flexible Declaration Scheme in 2017, allowing exporters and importers to declare transactions at customs offices other than where their shipments are stored. This study examines how its use changed after two major typhoons: Typhoon Jebi, which struck Kansai Airport in 2018, and Typhoon Faxai, which hit Narita Airport in 2019. Using transaction-level data, we find that utilization increased for both exports and imports following Kansai Airport’s closure, suggesting temporary adoption. After Faxai caused a power outage at Narita’s storage area, export utilization rose and remained high, albeit to a lesser extent than at Kansai Airport, indicating a more permanent shift.