| IATA | ICAO | Name | City | Type |
|---|---|---|---|---|
| AHI | WAPA | Amahai Airport | Amahai | Small Airport |
| - | WA1B | Aru Airport | Fekfetal / Jerdera-Trangan Island | Small Airport |
| NDA | WAPC | Bandanaira Airport | Bandanaira | Small Airport |
| BJK | WAPK | Benjina Airport | Maikoor Island | Small Airport |
| - | WAPB | Bula Airport | Bula | Small Airport |
| - | WAPL | Dumatubin Airport | Langgur | Small Airport |
| JIO | JIO | Jos Orno Imsula Airport | Tiakur | Small Airport Scheduled |
| LUV | WAPF | Karel Sadsuitubun Airport | Langgur | Medium Airport Scheduled |
| - | WAPU | Kufar Airport | - | Small Airport |
| - | WAPO | Larat Airport | Kepulauan Larat | Small Airport |
| SXK | WPAS | Mathilda Batlayeri Airport | Saumlaki-Yamdena Island | Small Airport Scheduled |
| - | WAPR | Namlea Airport | Namlea | Small Airport |
| NAM | WAPN | Namniwel Airport | Namniwel | Medium Airport Scheduled |
| NRE | WAPG | Namrole Airport | Namrole | Small Airport |
| AMQ | WAPP | Pattimura International Airport | Ambon | Medium Airport Scheduled |
| DOB | WAPD | Rar Gwamar Airport | Dobo-Warmar Island | Small Airport |
| - | WAPI | Saumlaki/Olilit Airport | Saumlaki-Yamdena Island | Small Airport |
| - | ID-0018 | Selaru Airstrip | Selaru Island | Closed Airport |
| WBA | WAPV | Wahai Airport | Wahai | Small Airport |