Third class airports
These handle domestic feeder flights. There are currently fifty-two, with four more under construction (Kobe Airport, New Ishigaki Airport, New Tarama Airport, and Shizuoka Airport). Many third-class airports are small airstrips serving isolated islands of the archipelago.
- Aguni Airport, Okinawa prefecture (AGJ)
- Amami Airport, Okinawa prefecture (ASJ)
- Aomori Airport, Aomori, Aomori prefecture (AOJ)
- Fukue Airport, Fukue, Nagasaki prefecture (FUJ)
- Fukui Airport, Fukui, Fukui prefecture (FKJ)
- Fukushima Airport, Fukushima, Fukushima prefecture (FKS)
- Hachijojima Airport, Hachijojima, Tokyo (HAC)
- Hanamaki Airport, Hanamaki, Iwate prefecture (HNA)
- Hateruma Airport, Okinawa prefecture (HTR)
- Iejima Airport, Iejima, Okinawa prefecture (IEJ)
- Iki Airport, Nagasaki prefecture (IKI)
- Ishigaki Airport, Okinawa prefecture (ISG)
- Izumo Airport, Hikawa, Shimane prefecture (IZO)
- Kamigoto Airport, Nagasaki prefecture (***)
- Kerama Airport, Okinawa prefecture (KJP)
- Kikai Airport, Okinawa prefecture (KKX)
- Kita-Daito Airport, Okinawa prefecture (KTD)
- Kozushima Airport, Kozushima, Tokyo (***)
- Kumejima Airport, Okinawa prefecture (UEO)
- Matsumoto Airport, Matsumoto, Nagano prefecture (MMJ)
- Memanbetsu Airport, Memanbetsu, Hokkaido (MMB)
- Minami-Daito Airport, Okinawa prefecture (***)
- Miyakejima Airport, Miyakejima, Tokyo (MYE)
- Miyako Airport, Hirara, Okinawa prefecture (***)
- Monbetsu Airport, Monbetsu, Hokkaido (MBE)
- Nakashibetsu Airport, Nakashibetsu, Hokkaido (SHB)
- Nanki-Shirahama Airport, Wakayama prefecture (SHM)
- Niijima Airport, Niijima, Tokyo (***)
- Noto Airport, Wajima, Ishikawa prefecture (***)
- Odate-Noshiro Airport, Akita prefecture (***)
- Ojika Airport, Nagasaki prefecture (***)
- Okayama Airport, Okayama, Okayama prefecture (OKJ)
- Oki Airport, Oki, Shimane prefecture (OKI)
- Okierabu Airport, Kagoshima prefecture (***)
- Okushiri Airport, Okushiri, Hokkaido (OIR)
- Oshima Airport, Oshima, Tokyo (OIM)
- Rebun Airport, Rebun, Hokkaido (RBJ)
- Rishiri Airport, Rishiri, Hokkaido (RIS)
- Sado Airport, Ryotsu, Niigata prefecture (SDS)
- Saga Airport, Saga, Saga prefecture (***)
- Shimojishima Airport, Okinawa prefecture (SHI)
- Shonai Airport, Sakata, Yamagata prefecture (SYO)
- Tanegashima Airport, Tanegashima, Kagoshima prefecture (***)
- Tarama Airport, Okinawa prefecture (***)
- Tokunoshima Airport, Tokunoshima, Kagoshima prefecture (***)
- Tottori Airport, Tottori, Tottori prefecture (TTJ)
- Toyama Airport, Toyama, Toyama prefecture (TOY)
- Tsushima Airport, Tsushima, Nagasaki prefecture (***)
- Yakushima Airport, Kagoshima prefecture (KUM)
- Yonaguni Airport, Okinawa prefecture (OGN)
- Yoron Airport, Kagoshima prefecture (***)