| Narita International Airport NRT | Tokyo | 122 |
| Tokyo Haneda International Airport HND | Tokyo | 104 |
| Kansai International Airport KIX | Osaka | 71 |
| Chubu Centrair International Airport NGO | Nagoya | 51 |
| Fukuoka Airport FUK | Fukuoka | 50 |
| New Chitose Airport CTS | Sapporo | 45 |
| Naha International Airport OKA | Okinawa (Naha) | 44 |
| Osaka Itami International Airport ITM | Osaka | 30 |
| Kagoshima Airport KOJ | Kagoshima | 19 |
| Kobe Airport UKB | Kobe | 18 |
| Sendai Airport SDJ | Sendai | 15 |
| Kumamoto Airport KMJ | Kumamoto | 14 |
| Hiroshima Airport HIJ | Hiroshima | 12 |
| New Ishigaki Airport ISG | Ishigaki | 12 |
| Amami Airport ASJ | Amami | 11 |
| Niigata Airport KIJ | Niigata | 11 |
| Sapporo Okadama Airport OKD | Sapporo | 11 |
| Matsuyama Airport MYJ | Matsuyama | 10 |
| Nagasaki Airport NGS | Nagasaki | 10 |
| Shimojishima Airport SHI | Miyakojima | 10 |
| Hakodate Airport HKD | Hakodate | 9 |
| Miyazaki Airport KMI | Miyazaki | 9 |
| Nagoya Airport / JASDF Komaki Air Base NKM | Nagoya | 9 |
| Kochi Ryoma Airport KCZ | Nankoku | 8 |
| Komatsu Airport / JASDF Komatsu Air Base KMQ | Kanazawa | 8 |
| Miyako Airport MMY | Miyakojima | 8 |
| Mount Fuji Shizuoka Airport FSZ | Makinohara / Shimada | 8 |
| Takamatsu Airport TAK | Takamatsu | 8 |
| Aomori Airport AOJ | Aomori | 7 |
| Izumo Enmusubi Airport IZO | Izumo | 7 |
| Akita Airport AXT | Akita | 6 |
| Ibaraki Airport IBR | Omitama | 6 |
| Iwate Hanamaki Airport HNA | Hanamaki | 6 |
| Kitakyushu Airport KKJ | Kitakyushu | 6 |
| Kushiro Airport KUH | Kushiro | 6 |
| Oita Airport OIT | Oita | 6 |
| Okayama Momotaro Airport OKJ | Okayama | 6 |
| Asahikawa Airport AKJ | Higashikagura | 5 |
| Memanbetsu Airport MMB | Ōzora | 5 |
| Okinoerabu Airport OKE | Wadomari | 4 |
| Shinshu-Matsumoto Airport MMJ | Matsumoto | 4 |
| Tokushima Awaodori Airport / JMSDF Tokushima Air Base TKS | Tokushima | 4 |
| Toyama Kitokito Airport TOY | Toyama | 4 |
| Yamagata Airport GAJ | Higashine | 4 |
| Fukushima Airport FKS | Sukagawa | 3 |
| Kyushu Saga International Airport HSG | Saga | 3 |
| Misawa Airport / Misawa Air Base MSJ | Misawa | 3 |
| Nakashibetsu Airport SHB | Nakashibetsu | 3 |
| New Tanegashima Airport TNE | Tanegashima | 3 |
| Tokachi-Obihiro Airport OBO | Obihiro | 3 |
| Tokunoshima Airport TKN | Amagi | 3 |
| Yakushima Airport KUM | Yakushima | 3 |
| Yonago Kitaro Airport / JASDF Miho Air Base YGJ | Yonago | 3 |
| Yoron Airport RNJ | Yoron | 3 |
| Amakusa Airport AXJ | Amakusa | 2 |
| Fukue Airport FUJ | Goto | 2 |
| Iwakuni Kintaikyo Airport IWK | Iwakuni | 2 |
| Iwami Airport IWJ | Masuda | 2 |
| Kikai Airport KKX | Kikai | 2 |
| Kumejima Airport UEO | Kumejima | 2 |
| Oki Global Geopark Airport OKI | Okinoshima | 2 |
| Okushiri Airport OIR | Okushiri Island | 2 |
| Rishiri Airport RIS | Rishiri | 2 |
| Shonai Airport SYO | Shonai | 2 |
| Tsushima Airport TSJ | Tsushima | 2 |
| Wakkanai Airport WKJ | Wakkanai | 2 |
| Yonaguni Airport OGN | Yonaguni | 2 |
| Hachijojima Airport HAC | Hachijojima | 1 |
| Iki Airport IKI | Iki | 1 |
| Kitadaito Airport KTD | Kitadaitōjima | 1 |
| Konotori Tajima Airport TJH | Toyooka | 1 |
| Minamidaito Airport MMD | Minamidaito | 1 |
| Miyakejima Airport MYE | Miyakejima | 1 |
| Monbetsu Airport MBE | Monbetsu | 1 |
| Nanki Shirahama Airport SHM | Shirahama | 1 |
| Noto Satoyama Airport NTQ | Wajima | 1 |
| Odate Noshiro Airport ONJ | Kitaakita | 1 |
| Oshima Airport OIM | Izu Oshima | 1 |
| Tarama Airport TRA | Tarama | 1 |
| Tottori Sand Dunes Conan Airport TTJ | Tottori | 1 |
| Yamaguchi Ube Airport UBJ | Ube | 1 |
| Aguni Airport AGJ | Aguni | — |
| Kadena Air Base DNA | Okinawa | — |
| Sado Airport SDS | Sado | — |