| Name | Type | IATA | ICAO | City |
|---|---|---|---|---|
| AA Bere Tallo (Haliwen) Airport | Small Airport Scheduled | ABU | WATA |
Atambua |
| Alor Island - Mali Airport | Small Airport Scheduled | ARD | WATM |
Kabola |
| Bajawa Soa (Turelelo) Airport | Small Airport | BJW | WATB |
Soa, Ngada |
| David Constantijn Saudale Airport | Small Airport | RTI | WATR |
Ba'a - Rote Island |
| El Tari Airport | Small Airport Scheduled | KOE | WATT |
Kupang |
| Frans Sales Lega Airport | Small Airport Scheduled | RTG | WATG |
Satar Tacik, Manggarai |
| Frans Xavier Seda Airport | Small Airport Scheduled | MOF | WATC |
Waioti |
| H. Hasan Aroeboesman (Ende) Airport | Small Airport Scheduled | ENE | WATE |
Ende |
| John Becker Airport | Small Airport | - | WATQ |
Pur-Pura |
| Kalabahi Airport | Closed Airport | - | ID-0337 |
Kalabahi |
| Komodo Airport | Small Airport Scheduled | LBJ | WATO |
Labuan Bajo, Manggarai Barat |
| Larantuka Gewayentana Airport | Small Airport Scheduled | LKA | WATL |
Tiwatobi |
| Mena Airport | Small Airport | - | WRKJ |
Mena-Timor Island |
| Naikliu Airport | Small Airport | - | WRKN |
Naikliu-Timor Island |
| Pantar Kabir Airport | Small Airport | AXO | AXO |
Kabir |
| Sabu-Tardanu Airport | Small Airport | SAU | WATS |
Sabu-Sawu Island |
| Tambolaka Airport | Small Airport Scheduled | TMC | WADT |
Radamata |
| Umbu Mehang Kunda Airport | Small Airport Scheduled | WGP | WADW |
Waingapu-Sumba Island |
| Wonopito Airport | Small Airport | LWE | WATW |
Lewoleba |