Comparing with airport traffic data stat in Japan in year 2023 (【最新】2023年度・令和5年度 日本の空港旅客数ランキング！ | 未来へ羽ばたく神戸空港), there are three airports with only charter flights now missing from the game: A map from the Great Circle Mapper - Great Circle Mapper .
Also for passenger traffic data (Note that traffic in Japan haven’t fully recovered in year 2023 so it’s only for comparison against each others), there are some airports that have traffic data which seems not quite consistent with other airports in the class:
| Airport | ICAO | Pax number | Pax Class |
|---|---|---|---|
| Tokyo Haneda | RJTT | 80,859,391 | pax 10 |
| Tokyo Narita | RJAA | 33,813,616 | pax 10 |
| Osaka Kansai | RJBB | 25,802,058 | pax 9 |
| Fukuoka | RJFF | 24,937,755 | pax 9 |
| Sapporo Chitose | RJCC | 22,933,393 | pax 9 |
| Okinawa | ROAH | 19,485,893 | pax 8 |
| Osaka Itami | RJOO | 14,793,159 | pax 8 |
| Nagoya Chubu Centrair | RJGG | 9,172,903 | pax 7 |
| Kagoshima | RJFK | 5,549,841 | pax 6 |
| Sendai | RJSS | 3,550,095 | pax 6 |
| Kobe | RJBE | 3,443,796 | pax 5 |
| Kumamoto | RJFT | 3,335,476 | pax 5 |
| Miyazaki | RJFM | 3,067,906 | pax 5 |
| Nagasaki | RJFU | 2,861,852 | pax 5 |
| Matsuyama | RJOM | 2,831,733 | pax 5 |
| Hiroshima International | RJOA | 2,685,855 | pax 5 |
| Ishigaki | ROIG | 2,609,612 | pax 5 |
| Takamatsu | RJOT | 1,847,502 | pax 5 |
| Oita | RJFO | 1,762,278 | pax 5 |
| Miyako Shima | ROMY | 1,755,051 | pax 4 |
| Hakodate | RJCH | 1,668,031 | pax 4 |
| Kochi, JP | RJOK | 1,609,984 | pax 4 |
| Komatsu | RJNK | 1,434,708 | pax 5 |
| Okayama | RJOB | 1,283,730 | pax 4 |
| Akita | RJSK | 1,208,568 | pax 4 |
| Kita Kyushu | RJFR | 1,187,091 | pax 4 |
| Aomori | RJSA | 1,169,438 | pax 4 |
| Niigata | RJSN | 1,056,208 | pax 4 |
| Tokushima | RJOS | 1,054,468 | pax 4 |
| Asahikawa | RJEC | 1,049,553 | pax 4 |
| Izumo | RJOC | 1,015,147 | pax 4 |
| Nagoya Komaki | RJNA | 940,546 | pax 4 |
| Ube | RJDC | 869,944 | pax 4 |
| Amami O Shima | RJKA | 869,068 | pax 4 |
| Memanbetsu | RJCM | 768,046 | pax 4 |
| Ibaraki | RJAH | 748,396 | pax 4 |
| Kushiro | RJCK | 727,151 | pax 4 |
| Obihiro | RJCB | 651,197 | pax 4 |
| Yonago | RJOH | 575,173 | pax 4 |
| Saga | RJFS | 532,259 | pax 4 |
| Shizuoka | RJNS | 525,631 | pax 4 |
| Hanamaki | RJSI | 483,044 | pax 4 |
| Iwakuni | RJOI | 474,004 | pax 4 |
| Sapporo Okadama | RJCO | 438,612 | pax 3 |
| Shimojishima | RORS | 424,286 | pax 1 |
| Tottori | RJOR | 375,803 | pax 4 |
| Toyama | RJNT | 370,524 | pax 4 |
| Yamagata | RJSC | 365,730 | pax 4 |
| Shonai | RJSY | 348,101 | pax 4 |
| Misawa | RJSM | 330,278 | pax 3 |
| Matsumoto | RJAF | 256,740 | pax 3 |
| Tsushima | RJDT | 251,845 | pax 4 |
| Fukushima | RJSF | 232,217 | pax 3 |
| Nanki Shirahama | RJBD | 229,703 | pax 3 |
| Kumejima | ROKJ | 220,176 | pax 3 |
| Hachijojima | RJTH | 206,080 | pax 4 |
| Tokunoshima | RJKN | 204,078 | pax 3 |
| Yakushima | RJFC | 197,804 | pax 3 |
| Nakashibetsu | RJCN | 197,372 | pax 3 |
| Odate Noshiro | RJSR | 177,025 | pax 2 |
| Fukue | RJFE | 174,819 | pax 4 |
| Wakkanai | RJCW | 171,241 | pax 3 |
| Iwami | RJOW | 133,564 | pax 3 |
| Wajima Noto | RJNW | 115,121 | pax 2 |
| Yonaguni Jima | ROYN | 114,117 | pax 2 |
| Okino Erabu | RJKB | 113,187 | pax 2 |
| Tanegashima | RJFG | 110,023 | pax 3 |
| Tokyo Chofu | RJTF | 105,983 | pax 1 |
| Yoronjima | RORY | 88,106 | pax 2 |
| Kikaiga Shima | RJKI | 83,613 | pax 2 |
| Oki | RJNO | 70,580 | pax 2 |
| Monbetsu | RJEB | 66,428 | pax 2 |
| Rishiri | RJER | 54,986 | pax 2 |
| Minamidaito | ROMD | 49,212 | pax 1 |
| Taramajima | RORT | 44,485 | pax 2 |
| Amakusa | RJDA | 44,437 | pax 1 |
| Toyooka | RJBT | 38,732 | pax 1 |
| Iki | RJDB | 34,828 | pax 2 |
| Niijima | RJAN | 34,173 | pax 1 |
| Miyakejima | RJTQ | 31,062 | pax 3 |
| Kitadaito | RORK | 27,688 | pax 1 |
| Kozujima | RJAZ | 26,483 | pax 1 |
| Oshima | RJTO | 25,006 | pax 2 |
| Okushiri | RJEO | 15,690 | pax 1 |
| Aguni | RORA | 1,245 | pax 1 |
| Iejima | RORE | 504 | N/A |
| Hateruma | RORH | 191 | pax 1 |
| Kerama | ROKR | 122 | pax 1 |
| Kohnan | RJBK | 19 | N/A |
| Oita kenou | ? | 2 | N/A |
| Sado Shima | RJSD | 0 | pax 1 |
Note that, Shimojishima airport have attracted numerous airlines in the past decade and now have multiple scheduled domestic and international flights everyday. While Komatsu airport have see traffic drop since opening of Hokuriku Shinkansen to Kanazawa last decade. With the Hokuriku Shinkansen further extended in the region and its effect on the airport need further observation.
In addition, according to various other sources, while not included in the national traffic data stat above, Suwanosejima airfield is an airfield in Japan that have scheduled charter to KOJ by New Japan Aviation on Cessna 172 since 2022, and the airlines also operated Cessna 172 flights to Satsumaiojima Airfield but paused since 2023 due to poor runway condition there as per Wikipedia.