Customs, Immigration and Quarantine (CIQ) is available at Japan’s Airports of Entry (AOE); CIQ service may be available to process flights at non-CIQ airports, but this must be requested and agreed in advance with authorities. At Japan’s airports, business jet travelers are generally processed alongside passengers from commercial flights in the main terminal. Setting a flight arrival time during non-peak hours helps ensure that your passengers are processed more quickly. Tokyo’s airports can arrange for CIQ processing for business jet passengers via the general aviation terminals at Tokyo’s Haneda and Narita airports, but this service must be arranged in advance and at additional expense.
Valid passports are required for passengers and crew members entering Japan. Visa requirements for passengers are subject to nationality and visas-on-arrival are not available in Japan at this time. Please refer to the Ministry of Foreign Affairs website Exemption of Visa page. For crew members, visas are not required because a crew shore pass can be issued by Immigrations upon arrival. Crew members must have valid crew ID and must be listed on the GenDec. This allows crew to stay in Japan for 7 nights/8 days for single port entry, and 15 days for multiple port entries.
See the below links for more information pertaining to the COVID-19 pandemic
–Procedures and Documents required to enter Japan