| IATA | ICAO | Name | City | Type |
|---|---|---|---|---|
| ABU | WATA | AA Bere Tallo (Haliwen) Airport | Atambua | Small Airport Scheduled |
| MLG | WARA | Abdul Rachman Saleh Airport | Malang | Medium Airport Scheduled |
| RSK | WASC | Abresso Airport | Ransiki-Papua Island | Small Airport |
| SRG | WARS | Achmad Yani Airport | Semarang | Medium Airport Scheduled |
| SOC | WARQ | Adisumarmo Airport | Surakarta | Medium Airport Scheduled |
| JOG | WARJ | Adisutjipto Airport | Yogyakarta | Medium Airport Scheduled |
| AEG | WIME | Aek Godang Airport | Padang Sidempuan | Medium Airport |
| AAP | WALS | Aji Pangeran Tumenggung Pranoto International Airport | Samarinda | Medium Airport Scheduled |
| LSR | WIMU | Alas Leuser Airport | Kutacane | Medium Airport Scheduled |
| ARD | WATM | Alor Island - Mali Airport | Kabola | Small Airport Scheduled |
| AHI | WAPA | Amahai Airport | Amahai | Small Airport |
| MXB | WAFM | Andi Jemma Airport | Masamba | Small Airport |
| AGD | ID-AGD | Anggi Airport | Anggi-Papua Island | Small Airport |
| AAS | ID-AAS | Apalapsili Airport | Apalapsili | Small Airport |
| APD | WAWN | Arung Palakka Airport | Bone | Small Airport |
| AKQ | ID-AKQ | Astra Ksetra Airport | Menggala | Small Airport |
| PXA | WIPY | Atung Bungsu Airport | Bentayan | Small Airport |
| AYW | WASA | Ayawasi Airport | Ayawasi | Small Airport |
| BXB | WASO | Babo Airport | Babo | Medium Airport |
| BXD | WAKE | Bade Airport | Bade | Small Airport |
| BJW | WATB | Bajawa Soa (Turelelo) Airport | Soa, Ngada | Small Airport |
| NAF | ID-NAF | Banaina Airport | Banaina-Borneo Island | Small Airport |
| NDA | WAPC | Bandanaira Airport | Bandanaira | Small Airport |
| BWX | WADY | Banyuwangi Airport | Rogojampi, Banyuwangi | Small Airport Scheduled |
| BXM | WAJG | Batom Airport | Batom | Small Airport |
| BJK | WAPK | Benjina Airport | Maikoor Island | Small Airport |
| BTW | WAOC | Bersujud Airport | Batu Licin | Small Airport Scheduled |
| BUW | WAWB | Betoambari Airport | Bau Bau | Small Airport |
| UGU | ID-ZGP | Bilogai-Sugapa Airport | Sugapa | Medium Airport Scheduled |
| GNS | WIMB | Binaka Airport | Gunungsitoli | Medium Airport Scheduled |
| GYO | ID-0214 | Blangkejeren Airport | Kabupaten Gayo Lues | Small Airport |
| BUI | WAJB | Bokondini Airport | Bokondini | Small Airport Scheduled |
| LKM | WAMI | Bolaang Mongondow Airport | Lolak | Small Airport Scheduled |
| LLO | WAFD | Bua - Palopo Lagaligo Airport | Palopo | Small Airport Scheduled |
| RTO | WICB | Budiarto Airport | Tangerang-Java Island | Small Airport |
| PGQ | WAME | Buli Airport | Pekaulang | Small Airport |
| BYQ | WALV | Bunyu Airport | Bunju Island | Small Airport |
| UOL | WAFY | Buol - Pogogul Airport | Buol-Celebes Island | Small Airport Scheduled |
| TSY | WICM | Cibeureum Airport | Tasikmalaya-Java Island | Small Airport |
| MEQ | WITC | Cut Nyak Dhien Airport | Kuala Pesisir | Medium Airport Scheduled |
| SIQ | WIDS | Dabo Airport | Pasirkuning-Singkep Island | Small Airport |
| DRH | WAJC | Dabra Airport | Dabra | Small Airport |
| DTD | WALJ | Datadawai Airport | Datadawai-Borneo Island | Small Airport Scheduled |
| RTI | WATR | David Constantijn Saudale Airport | Ba'a - Rote Island | Small Airport |
| WET | WABG | Deiyai / Waghete Baru Airport | Tigi | Small Airport |
| DPS | WADD | Denpasar I Gusti Ngurah Rai International Airport | Kuta, Badung | Large International Airport Scheduled |
| KRC | ID-KRC | Departi Parbo Airport | Sungai Penuh | Small Airport Scheduled |
| PGK | WIPK | Depati Amir Airport | Pangkal Pinang | Medium Airport Scheduled |
| KWB | WAHU | Dewadaru Airport | Karimunjawa | Small Airport Scheduled |
| DHX | ID-0277 | Dhoho International Airport | Kediri | Large International Airport |