Indonesia has thousands of Museums and cultural heritage sites. Following is only a partial list taken from the Wikipedia:

 North Jakarta and Thousand Islands

1. Maritime Museum
2. Onrust Archaeology Park

Indonesian Museum

• Jakarta Old Town
  • Bank Indonesia Museum
  • Bank Mandiri Museum
  • Fine Art and Ceramic Museum
  • Jakarta History Museum or Museum Fatahillah
  • Wayang Museum
• Jakarta Textile Museum

Central Jakarta

1. Gedung Joang ’45
2. Gedung Kesenian Jakarta
3. Gedung Mohammad Hoesni Thamrin
4. Jakarta Cathedral Museum
5. Jakarta Planetarium
6. Monas
7. Museum Adam Malik (1985, closed in 2005)^[6]
8. Museum Anatomy Fakultas Kedokteran Universitas Indonesia
9. Museum Jenderal Besar DR. Abdul Haris Nasution
10. Museum Kebangkitan Nasional
11. Museum Pers ANTARA
12. Museum Perumusan Naskah Proklamasi (the site where the text of the nation’s proclamation of independence was composed in 1945)
13. Museum Puri Bhakti Renatama
14. National Gallery of Indonesia
15. National Museum or Museum Gajah

National Museum of Press in Solo.

• Museum Sasmita Loka Jenderal Ahmad Yani
• Sumpah Pemuda Museum
• Taman Prasasti Museum

East Jakarta

• Museum Loka Jala Srana
• Museum of PKI Treason
• Monument of Sacred Pancasila
• Taman Mini Indonesia Indah
  • Asmat Museum
  • Indonesia Fauna Museum
  • Indonesia Museum
  • Istiqlal Museum
  • Indonesia Soldiership Museum
  • Insect Museum and Butterfly Park
  • Komodo Museum and Reptile Park
  • Museum of Electricity and New Energy
  • Oil and Natural Gas Museum
  • Sports Museum
  • Lighting Museum
  • Museum of Science and Technology
  • Indonesia Stamp Museum
  • Purna Bhakti Pertiwi Museum
  • Heirloom Museum
  • Telecommunication Museum
  • Timor Timur Museum
  • Transport Museum

Oei Hong Djien Museum, Indonesia

1. Reksa Artha Museum
2. Satrian Mandala Museum
3. Waspada Purbawisesa Museum
4. Ragunan Zoo

Yogyakarta

• Affandi Museum
• Batik Museum
• Fort Vredeburg Museum
• Hamengkubuwono IX Museum
• Kraton Yogyakarta Museum
• Yogya Kembali Museum, Sleman Regency
• Museum Sasmitaloka Panglima Besar Jenderal Soedirman
• Prambanan Museum
• Sana Budaya Museum (1939)

Sana Budaya Museum (1939)

• Ullen Sentalu Museum
• Wayang Kekayon Museum

Java

Asian–African Conference Museum, Bandung

1. Bandung Geological Museum, Bandung (1928)
2. Bandung Zoo, Bandung (1933)
3. Barli Museum, Bandung
4. Bogor Zoological Museum, Bogor (1894)
6. Indonesia Post Museum, Bandung
7. Kraton Kacirebonan Museum, Cirebon
8. Museum Prabu Geusan Ulun, Purwakarta
9. Museum Tanah Nasrel, Bogor
10. Percandian Batujaya Museum, Karawang
11. Wangsit Mandala Siliwangi Museum

Educational Museum

• Ambarawa Railway Museum, Ambarawa
• Indonesian Record Museum
• Keraton Surakarta Museum
• Kretek Museum, Semarang
• National Museum of Press, Solo
• Pekalongan Batik Museum, Pekalongan (1972)
• Radya Pustaka Museum (1890)
• Borobudur Museum
• Samudra Raksa Museum
• Ronggo Warsito State Museum, Semarang

1. Brawijaya Museum, Malang
2. Mpu Tantular State Museum
3. Museum Tugu Pahlawan, Surabaya
4. Trowulan Museum, Trowulan (1987)

Lesser Sunda Islands

Bali

1. Agung Rai Museum of Art
2. Bali Museum (1930)
3. Blanco Renaissance Museum
4. Buleleng Museum, Singaraja
5. Le Mayeur Museum, Sanur
6. Museum Rudana
7. Museum Semarajaya
8. Neka Art Museum, Ubud (1982)^[7]
9. Purbakala Archaeological Museum
10. Puri Lukisan Museum

West Nusa Tenggara

• West Nusa Tenggara State Museum (1982)

East Nusa Tenggara

• East Nusa Tenggara State Museum

Aceh

• Aceh Museum, Banda Aceh (1915)

Aceh Tsunami Museum, Banda Aceh.

• Aceh Tsunami Museum, Banda Aceh (2009)

Aceh Museum

North Sumatra

• Batak Museum, Balige
• Museum Pusaka Nias, Nias (1993).
• Zoological Museum of Pematangsiantar, Pematangsiantar (1936)
• North Sumatra Museum, Medan (1982)
• TB Silalahi Center, Balige Subdistrict (2008)

Riau and Riau Islands

• Museum Sang Nila Utama, Pekanbaru (1994)
• Museum Istana Siak Sri Indrapura, Indrapura (Building from 1889)
• Museum Sultan Sulaiman Badrul Alamsyah, Tanjung Pinang

West Sumatra

• Adityawarman Museum, Padang (1977)
• Museum Rumah Kelahiran Buya Hamka, Agam (2001)

Rumah Gadang, a traditional Minang house of West Sumatra

• Tri Daya Eka Dharma Museum, Bukittinggi
• Gedung Joang ’45, Padang
• Goedang Ransoem Museum, Sawahlunto
• Galeri Tambang Mbah Soero, Sawahlunto
• Information Center of Minangkabau Culture, Padang Panjang (1990)
• Railway Museum, Sawahlunto
• Bukittinggi Zoological Museum, Bukittinggi

Bengkulu

• Bengkulu State Museum
• Fort Marlborough, Bengkulu City

Jambi

• Jambi Museum, Jambi City (1988)
• Muaro Jambi Temple Compounds Site Museum, Muaro Jambi Regency
• Museum Perjuangan Rakyat Jambi, Jambi City (1993)

South Sumatra and Bangka–Belitung Islands

• Balaputradewa Museum, Palembang
• Museum UPT Belitung, Belitung
• Sriwijaya Museum, Sriwijaya Kingdom Archaeological Park, Palembang
• Sultan Mahmud Badaruddin II Museum, Palembang
• Textile Museum, Palembang

Lampung

• Ruwa Jurai Museum, Bandar Lampung (1988)

Kalimantan

• Balanga Museum, Palangkaraya
• Kayu Sampit Museum, East Kotawaringin Regency
• Lewu Hante Museum, Pasar Panas, East Barito Regency
• Kalimantan Art Gallery, Samarinda
• Mulawarman State Museum, Tenggarong Subdistrict
• Candi Agung Museum, Amuntai, North Hulu Sungai Regency
• Lambung Mangkurat State Museum, Banjarbaru

Wasaka Museum in Banjarmasi

• Wasaka Museum, Banjarmasin

• West Kalimantan State Museum, Pontianak

 Sulawesi

• Museum Batara Guru, Wara Utama Subdistrict
• Museum La Galigo, Fort Rotterdam, Makassar
• Buton Palace Museum, Baubau, Buton Island
• Southeast Sulawesi State Museum, Kendari

Maluku

• Siwa Lima State Museum, Ambon (1973)
• Kedaton Sultan Ternate Museum, Kota Ternate Utara Subdistrict(1982, building is from 1813)

Papua

• Asmat Museum of Culture and Progress, Agats (1973)

Read about many more HERE