- Destinations Terminated Destinations
{{unreferenced|date=December 2012}}The former Indonesian airline Merpati Nusantara Airlines offered flights to many domestic destinations and to Timor Leste, Australia, Philippines, Malaysia and Singapore. Destinations- {{flag|Indonesia}}
- Alor - Mali Airport
- Amahai - Amahai Airport
- Balikpapan - Sultan Aji Muhammad Sulaiman Airport
- Bajawa - Bajawa Soa Airport and Bajawa Pahdamaleda Airport
- Bandung - Husein Sastranegara International Airport
- Banjarmasin - Syamsudin Noor Airport
- Banyuwangi
- Batam - Hang Nadim Airport
- Biak - Frans Kaisiepo Airport
- Bima - Bima Airport
- Bintuni - Bintuni Airport
- Buol - Tolo-Toli Airport
- Denpasar - Ngurah Rai International Airport Hub
- Ende - H. Hasan Aroeboesman Airport
- Gorontalo - Jalaluddin Airport
- Jakarta
- Halim Perdanakusuma International Airport Secondary Hub
- Soekarno-Hatta International Airport Main Hub
- Jayapura - Sentani Airport
- Kaimana - Kaimana Airport
- Kambuaya - Kambuaya Airport
- Karubaga - Karubaga Airport
- Kebar - Kebar Airport
- Kendari - Haluoleo Airport
- Kepi - Kepi Airport
- Kimam - Kimam Airport
- Kisar - Kisar Airport
- Kupang - El Tari Airport
- Labuan Bajo - Komodo Airport
- Labuha - Usman Sadik Airport
- Langgur - Dumatubin Airport
- Larantuka - Gewayentana Airport
- Luwuk - Luwuk Airport
- Makassar - Sultan Hasanuddin International Airport Hub
- Mamuju - Tampa Padang Airport
- Manado - Sam Ratulangi International Airport
- Mangole - Mangole Airport
- Manokwari - Rendani Airport
- Mataram - Lombok International Airport
- Maumere - Wai Oti Airport
- Medan - Kuala Namu International Airport
- Melangguane - Melanggguane Airport
- Merauke - Mopah Airport
- Merdei - Merdei Airport
- Meulaboh - Meulaboh Airport
- Mulia - Mulia Airport
- Nabire - Nabire Airport
- Namlea - Namlea Airport
- Namrole - Namrole Airport
- Nias - Binaka Airport
- Okaba - Okaba Airport
- Oksibil - Oksibil Airport
- Padang - Minangkabau International Airport
- Palembang - Sultan Mahmud Badaruddin II Airport
- Palu - Mutiara Airport
- Pangkal Pinang - Depati Amir Airport
- Pekanbaru - Sultan Syarif Kasim II International Airport
- Poso - Kasiguncu Airport
- Ruteng - Ruteng Airport
- Sampit - Sampit Airport
- Sanana - Sanana Airport
- Sarmi - Sarmi Airport
- Saumlaki - Saumlaki Airport
- Sawu - Sawu Airport
- Senngo - Senggo Airport
- Sibolga - Sibolga Airport
- Sinabang - Sinabang Airport
- Sinak - Sinak Airport
- Semarang - Achmad Yani International Airport
- Sorong - Sorong Airport
- Surabaya - Juanda International Airport Hub
- Tanah Merah - Tanah Merah Airport
- Tanjung Karang - Radin Inten II Airport
- Tarakan - Juwata International Airport
- Teminabuan - Teminabuan Airport
- Ternate - Babullah Airport
- Timika - Timika Airport
- Tiom - Tiom Airport
- Tolitoli - Tolitoli Airport
- Waingapu - Waingapu Airport
- Wamena - Mau Hau Airport
- Yogyakarta - Adisucipto International Airport
Terminated Destinations- {{flag|Australia}}
- Sydney - Sydney International Airport
- Canberra - Canberra International Airport
- Perth - Perth International Airport
- {{flag|Malaysia}}
- Subang - Subang International Airport (later Kuala Lumpur International Airport formerly Subang International Airport)
- Kuala Lumpur - Kuala Lumpur International Airport
- Penang - Bayan Lepas International Airport
- {{flag|Philippines}}
- Cebu - Mactan-Cebu International Airport
- Davao - Francisco Bangoy International Airport
- {{flag|Singapore}}
- Singapore - Singapore Changi International Airport
- {{flag|Timor Leste}}
- Timor Leste - Presidente Nicolau Lobato International Airport
6 : Aviation in Australia|Aviation in East Timor|Aviation in Indonesia|Aviation in Malaysia|Aviation in Singapore|Merpati Nusantara Airlines |