| Island | City | Airport | Notes |
| Hokkaido | Hakodate | Hakodate Airport | |
| Hokkaido | Kushiro | Kushiro Airport | |
| Hokkaido | Monbetsu | Monbetsu Airport | |
| Hokkaido | Nakashibetsu | Nakashibetsu Airport | |
| Hokkaido | Ōzora | Memanbetsu Airport | |
| Hokkaido | Rishiri Island | Rishiri Airport | |
| Hokkaido | Sapporo | New Chitose Airport | |
| Hokkaido | Wakkanai | Wakkanai Airport | |
| Honshu | Akita | Akita Airport | |
| Honshu | Aomori | Aomori Airport | |
| Honshu | Fukushima | Fukushima Airport | |
| Honshu | Hiroshima | Hiroshima Airport | |
| Honshu | Iwakuni | Marine Corps Air Station Iwakuni | |
| Honshu | Iwami | Iwami Airport | |
| Honshu | Kitaakita | Odate–Noshiro Airport | |
| Honshu | Komatsu | Komatsu Airport | |
| Honshu | Nagoya | Chūbu Centrair International Airport | |
| Honshu | Niigata | Niigata Airport | |
| Honshu | Okayama | Okayama Airport | |
| Honshu | Osaka | Kansai Airport | |
| Honshu | Osaka | Itami Airport | |
| Honshu | Sakata | Shonai Airport | |
| Honshu | Sendai | Sendai Airport | |
| Honshu | Tokyo | Haneda Airport | |
| Honshu | Tokyo | Narita International Airport | |
| Honshu | Tokyo | Oshima Airport | |
| Honshu | Tottori | Tottori Airport | |
| Honshu | Toyama | Toyama Airport | |
| Honshu | Yonago | Miho-Yonago Airport | |
| Kyushu | Fukuoka | Fukuoka Airport | |
| Kyushu | Gotō - Fukue | Fukue Airport | |
| Kyushu | Kagoshima | Kagoshima Airport | |
| Kyushu | Kumamoto | Kumamoto Airport | |
| Kyushu | Miyazaki | Miyazaki Airport | |
| Kyushu | Nagasaki | Nagasaki Airport | |
| Kyushu | Oita | Oita Airport | |
| Kyushu | Tsushima Island | Tsushima Airport | |
| Ryukyu Islands | Ishigaki | New Ishigaki Airport | |
| Ryukyu Islands | Miyakojima | Miyako Airport | |
| Ryukyu Islands | Naha | Naha Airport | |
| Shikoku | Kōchi | Kōchi Airport | |
| Shikoku | Matsuyama | Matsuyama Airport | |
