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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.

 Indonesia

• 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
  • Halim Perdanakusuma International Airport (Base)
  • Soekarno-Hatta International Airport (Base)
• 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

 Australia

• Sydney – Sydney Airport
• Darwin – Darwin International Airport
• Canberra – Canberra Airport
• Perth – Perth Airport

 Malaysia

• Kuala Lumpur
  • Sultan Abdul Aziz Shah Airport
  • Kuala Lumpur International Airport
• Penang – Penang International Airport

 Philippines

• Cebu – Mactan–Cebu International Airport
• Davao – Francisco Bangoy International Airport

 Singapore

• Changi Airport

 Timor Leste

• Dili – Presidente Nicolau Lobato International Airport