Airports
| Airport | IATA | Prefecture | Passengers/year | Role |
|---|---|---|---|---|
| Tokyo Haneda | HND | Tokyo | 78 000 000 | Hub |
| Tokyo Narita | NRT | Chiba | 37 000 000 | Hub |
| Kansai | KIX | Osaka | 30 000 000 | Hub |
| Fukuoka | FUK | Fukuoka | 25 000 000 | Hub |
| New Chitose | CTS | Hokkaido | 24 000 000 | Hub |
| Naha | OKA | Okinawa | 20 000 000 | Hub |
| Osaka Itami | ITM | Osaka | 16 000 000 | Hub |
| Chubu Centrair | NGO | Aichi | 12 000 000 | Hub |
| Kagoshima | KOJ | Kagoshima | 6 000 000 | Regional |
| Sendai | SDJ | Miyagi | 3 700 000 | Regional |
| Kumamoto | KMJ | Kumamoto | 3 400 000 | Regional |
| Nagasaki | NGS | Nagasaki | 3 300 000 | Regional |
| Miyazaki | KMI | Miyazaki | 3 300 000 | Regional |
| Kobe | UKB | Hyogo | 3 300 000 | Regional |
| Matsuyama | MYJ | Ehime | 3 000 000 | Regional |
| Ishigaki | ISG | Okinawa | 2 800 000 | Island |
| Hiroshima | HIJ | Hiroshima | 2 700 000 | Regional |
| Komatsu | KMQ | Ishikawa | 2 000 000 | Regional |
| Oita | OIT | Oita | 1 900 000 | Regional |
| Takamatsu | TAK | Kagawa | 1 900 000 | Regional |
| Miyako | MMY | Okinawa | 1 700 000 | Island |
| Hakodate | HKD | Hokkaido | 1 700 000 | Regional |
| Kitakyushu | KKJ | Fukuoka | 1 400 000 | Low-cost |
| Kochi | KCZ | Kochi | 1 400 000 | Regional |
| Okayama | OKJ | Okayama | 1 300 000 | Regional |
| Akita | AXT | Akita | 1 300 000 | Regional |
| Aomori | AOJ | Aomori | 1 100 000 | Regional |
| Niigata | KIJ | Niigata | 1 100 000 | Regional |
| Asahikawa | AKJ | Hokkaido | 1 100 000 | Regional |
| Tokushima | TKS | Tokushima | 1 100 000 | Regional |
| Yamaguchi Ube | UBJ | Yamaguchi | 900 000 | Regional |
| Izumo | IZO | Shimane | 900 000 | Regional |
| Saga | HSG | Saga | 900 000 | Low-cost |
| Amami | ASJ | Kagoshima | 800 000 | Island |
| Nagoya Komaki | NKM | Aichi | 800 000 | Regional |
| Shizuoka | FSZ | Shizuoka | 700 000 | Regional |
| Ibaraki | IBR | Ibaraki | 700 000 | Low-cost |
| Memanbetsu | MMB | Hokkaido | 700 000 | Regional |
| Yonago Kitaro | YGJ | Tottori | 700 000 | Regional |
| Kushiro | KUH | Hokkaido | 600 000 | Regional |
| Obihiro | OBO | Hokkaido | 600 000 | Regional |
| Iwakuni Kintaikyo | IWK | Yamaguchi | 600 000 | Regional |
| Hanamaki | HNA | Iwate | 500 000 | Regional |
| Toyama | TOY | Toyama | 500 000 | Regional |
| Tottori | TTJ | Tottori | 400 000 | Regional |
| Shonai | SYO | Yamagata | 400 000 | Regional |
| Yamagata | GAJ | Yamagata | 400 000 | Regional |
| Misawa | MSJ | Aomori | 300 000 | Regional |
| Tsushima | TSJ | Nagasaki | 300 000 | Island |
| Kumejima | UEO | Okinawa | 300 000 | Island |
| Fukushima | FKS | Fukushima | 250 000 | Regional |
| Wakkanai | WKJ | Hokkaido | 200 000 | Regional |
| Matsumoto | MMJ | Nagano | 200 000 | Regional |
| Nanki-Shirahama | SHM | Wakayama | 200 000 | Regional |
| Yakushima | KUM | Kagoshima | 200 000 | Island |
| Hachijojima | HAC | Tokyo | 150 000 | Island |
| Noto Satoyama | NTQ | Ishikawa | 150 000 | Regional |
| Odate-Noshiro | ONJ | Akita | 130 000 | Regional |
| Oki | OKI | Shimane | 80 000 | Island |
Passenger volumes are order-of-magnitude figures for the most recent available years, held for comparison rather than calculation: no single published series covers every field on one date. Airports are assigned to the prefecture they physically occupy, not the city in their name — Narita is in Chiba, not Tokyo.
From Tokyo
| Destination | Prefecture | Time from Tokyo | Service |
|---|---|---|---|
| Shin-Yokohama | Kanagawa | 0:18 | Shinkansen |
| Odawara – Hakone | Kanagawa | 0:35 | Shinkansen |
| Atami | Shizuoka | 0:37 | Shinkansen |
| Mishima | Shizuoka | 0:44 | Shinkansen |
| Utsunomiya – Nikko | Tochigi | 0:50 | Shinkansen |
| Takasaki | Gunma | 0:50 | Shinkansen |
| Shizuoka | Shizuoka | 1:00 | Shinkansen |
| Karuizawa | Nagano | 1:05 | Shinkansen |
| Nasushiobara | Tochigi | 1:10 | Shinkansen |
| Echigo-Yuzawa | Niigata | 1:15 | Shinkansen |
| Nagano | Nagano | 1:19 | Shinkansen |
| Hakone-Yumoto | Kanagawa | 1:25 | Limited express |
| Fukushima | Fukushima | 1:30 | Shinkansen |
| Hamamatsu | Shizuoka | 1:30 | Shinkansen |
| Sendai | Miyagi | 1:30 | Shinkansen |
| Nagoya | Aichi | 1:35 | Shinkansen |
| Niigata | Niigata | 1:40 | Shinkansen |
| Nikko – Tobu | Tochigi | 1:50 | Limited express |
| Toyama | Toyama | 2:08 | Shinkansen |
| Morioka | Iwate | 2:10 | Shinkansen |
| Kyoto | Kyoto | 2:12 | Shinkansen |
| Shin-Osaka | Osaka | 2:25 | Shinkansen |
| Kanazawa | Ishikawa | 2:30 | Shinkansen |
| Yamagata | Yamagata | 2:30 | Shinkansen |
| Shin-Kobe | Hyogo | 2:40 | Shinkansen |
| Fukui | Fukui | 2:55 | Shinkansen |
| Shin-Aomori | Aomori | 2:55 | Shinkansen |
| Himeji | Hyogo | 3:00 | Shinkansen |
| Okayama | Okayama | 3:10 | Shinkansen |
| Shinjo | Yamagata | 3:20 | Shinkansen |
| Ise-shi | Mie | 3:20 | Limited express |
| Akita | Akita | 3:50 | Shinkansen |
| Hiroshima | Hiroshima | 3:50 | Shinkansen |
| Shin-Hakodate-Hokuto | Hokkaido | 3:55 | Shinkansen |
| Takayama | Gifu | 4:10 | Limited express |
| Kokura | Fukuoka | 4:40 | Shinkansen |
| Hakata – Fukuoka | Fukuoka | 4:55 | Shinkansen |
| Kinosaki Onsen | Hyogo | 5:00 | Limited express |
| Kii-Katsuura | Wakayama | 5:30 | Limited express |
| Kumamoto | Kumamoto | 5:50 | Shinkansen |
| Kagoshima-Chuo | Kagoshima | 6:30 | Shinkansen |
| Izumo-shi – ночной поезд | Shimane | 12:00 | Limited express |
| Sapporo | Hokkaido | — | By air only |
| Naha | Okinawa | — | By air only |
| Matsuyama | Ehime | — | By air only |
| Takamatsu | Kagawa | — | By air only |
| Kochi | Kochi | — | By air only |
| Tokushima | Tokushima | — | By air only |
| Beppu – Oita | Oita | — | By air only |
| Nagasaki | Nagasaki | — | By air only |
| Miyazaki | Miyazaki | — | By air only |
| Ishigaki · Miyako | Okinawa | — | By air only |
| Naoshima – паром из Уно | Kagawa | — | By sea |
| Sado – паром из Ниигаты | Niigata | — | By sea |
| Yakushima – судно из Кагосимы | Kagoshima | — | By sea |
Minimum typical direct service. Categories differ by up to half an hour on the same route. A dash means there is no high-speed rail link and the route sells by air or sea — for the island prefectures that is the central fact, not a missing value.