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The former Indonesian airline Merpati Nusantara Airlines offered flights to many domestic destinations and to Timor Leste, Australia, Philippines, Malaysia and Singapore.
Destinations
- Alor – Mali Airport
- Ambon – Pattimura Airport
- Amahai – Amahai Airport
- Balikpapan – Sultan Aji Muhammad Sulaiman Sepinggan Airport
- Bajawa – Bajawa Soa Airport
- Bandung – Husein Sastranegara Airport
- Banjarmasin – Syamsudin Noor Airport
- Banyuwangi – Banyuwangi International Airport
- Batam – Hang Nadim International Airport
- Biak – Frans Kaisiepo Airport
- Bima – Bima Airport
- Bintuni – Steenkool Airport
- Buol – Tolo-Toli Airport
- Denpasar – I Gusti Ngurah Rai International Airport (Base)
- Ende – H. Hasan Aroeboesman Airport
- Gorontalo – Jalaluddin Airport
- Jakarta
- 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 International Airport
- Labuha – Usman Sadik Airport
- Langgur – Dumatubin Airport
- Larantuka – Gewayentana Airport
- Luwuk – Syukuran Aminuddin Amir Airport
- Makassar – Sultan Hasanuddin International Airport (Base)
- Mamuju – Tampa Padang Airport
- Manado – Sam Ratulangi International Airport
- Mangole – Mangole Airport
- Manokwari – Rendani Airport
- Mataram – Lombok International Airport
- Maumere – Wai Oti Airport
- Medan – Kualanamu 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 – Ferdinand Lumban Tobing Airport
- Sinabang – Sinabang Airport
- Sinak – Sinak Airport
- Semarang – Jenderal Ahmad Yani Airport
- Sorong – Domine Eduard Osok Airport
- Surabaya – Juanda International Airport (Base)
- 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 – Toli-Toli Airport
- Waingapu – Waingapu Airport
- Wamena – Mau Hau Airport
- Yogyakarta – Adisutjipto Airport
- Sydney – Sydney Airport
- Darwin – Darwin International Airport
- Canberra – Canberra Airport
- Perth – Perth Airport