| IATA | ICAO | Name | City | Type |
|---|---|---|---|---|
| - | MY-0015 | Hunter (Morotai) Airport | Morotai | Small Airport |
| - | MY-0016 | Jeroco Airport | Jeroco | Small Airport |
| - | MY-0017 | Kelabakan Airport | Kelabakan | Small Airport |
| KGU | WBKG | Keningau Airport | Keningau | Small Airport |
| - | WBKB | Kota Belud Airport | Kota Belud | Small Airport |
| BKI | WBKK | Kota Kinabalu International Airport | Kota Kinabalu | Medium Airport Scheduled |
| - | MY-0018 | Kuala Kahaba Airport | Kuala Kahaba | Small Airport |
| - | WBKU | Kuala Penyu Airport | Kuala Penyu | Small Airport |
| KUD | WBKT | Kudat Airport | Kudat | Small Airport Scheduled |
| LDU | WBKD | Lahad Datu Airport | Lahad Datu | Medium Airport Scheduled |
| LAC | LAC | Layang-Layang Airport | Pulau Layang-Layang (Swallow Reef) | Small Airport |
| GSA | WBKN | Long Pasia Airport | Long Miau | Small Airport |
| - | MY-0020 | Marak Parak Airport | Marak Parak | Small Airport |
| - | MY-0021 | Meligan Airport | Meligan | Small Airport |
| - | MY-0022 | Meridi Airport | Meridi | Small Airport |
| - | MY-0051 | Mostyn Airport | Mostyn | Closed Airport |
| - | MY-0023 | Nangoh Airport | Nangoh | Small Airport |
| PAY | WBKP | Pamol Airport | Pamol | Small Airport |
| - | MY-0024 | Pandewan Airport | Pandewan | Small Airport |
| RNU | WBKR | Ranau Airport | Ranau | Small Airport |
| SXS | WBKH | Sahabat [Sahabat 16] Airport | Sahabat | Small Airport |
| SDK | WBKS | Sandakan Airport | Sandakan | Medium Airport Scheduled |
| SMM | WBKA | Semporna Airport | Semporna | Small Airport |
| SPE | WBKO | Sepulot Airport | Sepulot | Small Airport |
| SPT | MY-SPT | Sipitang Airport | Sipitang | Small Airport |
| - | MY-0026 | Sook Airport | Sook | Small Airport |
| - | MY-0042 | Station Lima Helipad | Pulau Layang-Layang (Swallow Reef) | Heliport |
| - | MY-0002 | Station Mike Helipad | Terumbu Mantanani (Mariveles Reef) | Heliport |
| - | MY-0001 | Station Papa Helipad | Terumbu Peninjau (Investigator Shoal) | Heliport |
| - | MY-0043 | Station Sierra Helipad | Terumbu Siput (Erica Reef) | Heliport |
| - | MY-0010 | Station Uniform Helipad | Terumbu Ubi (Ardasier Reef) | Heliport |
| TWU | WBKW | Tawau Airport | Tawau | Medium Airport Scheduled |
| TEL | WBKE | Telupid Airport | Telupid | Small Airport |
| TMG | WBKM | Tomanggong Airport | Tomanggong | Small Airport Scheduled |
| - | MY-0027 | Ulu Tomani Airport | Ulu Tomani | Small Airport |
| - | MY-0028 | Wallace Bay Airport | Wallace Bay | Small Airport |