This website explains the screening process at Narita Airport.

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.

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.

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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