This website explains the screening process at Narita Airport.

To All Passengers Connecting at Narita Airport

Do you know why connecting passengers have to go through security screenings in Japan?

When traveling from an overseas airport via Narita to another overseas airport

Ex. Depart from the U.S., transfer in Japan, travel to South Korea

Criteria for security screening vary by country. Japan has its criteria, the U.S. has its criteria, South Korea has its criteria. Each country conducts its security screening differently. So even if you are just transiting, you will have to undergo screening according to Japanese criteria before you enter the departure area of a Japanese airport.
Please see the figure above.

Point1
First, before departing from the U.S., the passenger must undergo security screening according to U.S. criteria in order to enter the U.S. airport’s departure area. Only passengers who have undergone screening and cleared the U.S. criteria may depart.
Point2
After departing from the U.S., the passenger arrives at an airport in Japan (Narita Airport) for transit. What must be noted here is that the passenger in the arrival area has only been screened according to the U.S. criteria.
Point3
However, in order for the connecting passenger to enter the Narita Airport departure area, he or she must now undergo screening according to Japan criteria. Only passengers who have undergone screening and cleared the Japan criteria may depart for South Korea.

When traveling from an airport in Japan via Narita to an overseas airport

Ex. Depart from Osaka, transfer at Narita, travel to the U.S.

Due to the variations in security screenings criteria for domestic and international flights, you must undergo a security screening at Narita Airport before transiting to an international flight.
Please see the figure above.

Point1
First, before departing from Osaka Airport, the passenger must undergo security screening according to Japan domestic flight criteria in order to enter the Osaka Airport departure area. Only passengers who have undergone screening and cleared the domestic flight criteria may depart.
Point2
After departing Osaka Airport, the passenger arrives at Narita Airport for transit. What must be noted here is that the passenger in the arrival area has only been screened according to the Japan domestic flight criteria.
Point3
However, in order for the connecting passenger to enter the Narita Airport international departure area, he or she must now undergo screening according to international flight criteria. Only passengers who have undergone screening and cleared the international flight criteria may depart for the U.S.

When traveling from an overseas airport via Narita to an airport within Japan

Ex. Depart from Australia, transfer at Narita, travel to Hokkaido

If you are arriving at Narita Airport from overseas and transiting to a domestic flight, you must temporarily enter Japan and step inside the public area. Therefore, you will undergo an additional security screening before you board your domestic flight.
Please see the figure above.

Point1
First, before departing from the airport in Australia, the passenger must undergo security screening according to Australia criteria in order to enter the Australian airport departure area. Only passengers who have undergone screening and cleared the Australia criteria may depart.
Point2
After departing the Australian airport, the passenger arrives at Narita Airport for transit. Following passport control at Narita Airport, the passenger will enter the public area. At this point, he or she may come into contact with people or objects that have not cleared security screening.
Point3
Therefore, in order for the connecting passenger to enter the Narita Airport domestic departure area, he or she must now undergo screening according to Japan criteria. Only passengers who have undergone screening and cleared the Japan criteria may depart for Hokkaido.

When traveling from Narita Airport and connecting at an overseas airport

If you are departing Narita Airport and transferring at an overseas airport, the country in which you make the connection will have different security criteria than those of Japan, so you may be required to undergo a security screening at your connecting airport. For more information, please contact your airline.

When traveling from Narita Airport and connecting at an overseas airport

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