This website explains the screening process at Narita Airport.

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When arriving at Narita on an international flight and departing for an airport within Japan

Security screening is required at Narita Airport.

If you are departing from a country other than Japan, entering Japan via Narita Airport and connecting to a domestic flight, you will be required to temporarily enter the Public Area. Therefore, you must undergo an additional screening before boarding your domestic flight.

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You will need to collect your checked baggage upon entering Japan.

In compliance with the Customs Law, all passengers entering Japan must undergo a customs inspection. Therefore, all passengers entering Japan via Narita Airport in transit to domestic flights must collect their suitcases and other checked baggage.

What about liquors, perfumes and other duty-free items?

You can bring liquors, perfumes and other duty-free on board your flight.
There are no quantity restrictions for liquids on domestic flights within Japan.

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Carry-on items other than liquids will also be screened.

Carry-on liquid restrictions do not apply at the domestic screening areas. However, as with international flights, checks are conducted for prohibited items other than liquids in carry-on baggage.
For examples of prohibited items, see the Prohibited Carry-on Items List page.

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