According to CIA The World Factbook, there are 175 airports in Japan. Then, 142 of them are with paved runways.
The number of airports are 32nd in the world. The area is 63rd and the population is 11th in the world. Germany which is 64th in area and 18th in population has 318 airports with paved runways, which is more than a double of Japan. United Kingdom which is smaller in size and population than Germany but island nation similar to Japan has 271 airports with paved runways.
However, if you compare with airports with paved runways from 2428 to 3047 meters, Japan has 45, Germany has 49, and then United Kingdom has 29.
Total airports with paved runways
Over 3047 m
2438 - 3047 m
1524 - 2437 m
Runways over 3047 m are suitable for wide-body aircrafts which has two aisles. Especially 3047 m are needed for large wide-body aircrafts such as Airbus A380 and Boeing 747. Therefore airports with paved runway over 3047 meters can be classified as international airports with intercontinental flights.
Japan has 6 airports with paved runways over 3047 meters but two of them are US military bases. Therefore only 4 airports; Tokyo Haneda, Tokyo Narita, Kansai and Chubu are the ones which ordinary passengers can use.
From the comparison table, you can see that Japan has much more airports with paved runways between 2438 and 3047 meters which also suit for wide-body aircrafts but not such big as A380 or B747. Therefore these airports cane be classified as international airports.
2019's data from Ministry of Land, Infrastructure, Transport and Tourism.
International + Domestic flights
Then, not like Germany which population is not concentrated in capital Berlin or its surroundings, Japan's domestic flights are concentrated connecting Tokyo and other cities. Then, highest number of ridership is not flights between Tokyo and second largest metropolitan area in Japan, Osaka-Kyoto-Kobe. The busiest flights are between Tokyo and Sapporo, the prefectural capital of Hokkaido.
Naha airport is the gateway for Okinawa prefecture. Okinawa prefecture's population is just 1.46 million which is 25th in Japan. There are more domestic flights from Naha airport than Sapporo; Hokkaido prefectural capital. Even Hokkaido's population is 5.22 million. The main reason is that Hokkaido has less offshore islands than Okinawa and Hokkaido has railway connection. Travelers between Sapporo and other parts of Hokkaido can be by trains or buses. Therefore tourists from Tokyo or Osaka must take domestic flights if they want to visit Okinawa(however, there is a ferry from Kagoshima in Kyushu island but the port of more than 1000 km away from Tokyo).
Airports in Greater Tokyo metropolitan area.
Distance from downtown Tokyo
Mainly domestic flights
Mainly international flights.
Flights to offshore islands only.
Only Haneda and Narita airports have railway connections.
Airports in Osaka-Kyoto-Kobe metropolitan area.
Distance from Kyoto station
Osaka - Itami
Domestic flights only
Osaka - Kansai
International flights mainly
Domestic flights only
No regular flights
All airports except Yao have railway connections.
Airports in Japan with railway connections.
Sapporo - Shin-Chitose