Currently: * Malabar danio (Devario malabaricus) - Taman Mini Indonesia Indah * Indian star tortoise (Geochelone elegans) - Taman Safari Bogor * Common leopard gecko (Eublepharis macularius) - Taman Mini Indonesia Indah and Lembang Park & Zoo * Rose-ringed parakeet (Psittacula krameri) - Royal Safari Garden * Nicobar pigeon (Caloenas nicobarica) - Taman Safari Bogor * Indian peafowl (Pavo cristatus) - Almost every Indonesian zoo * Bar-headed goose (Anser indicus) - Batu Secret Zoo * Demoiselle crane (Grus virgo) - Taman Safari Bogor * Small Indian civet (Viverricula indica) - Taman Safari Bogor * Chital (Axis axis) - Almost every Indonesian zoo * Blackbuck (Antilope cervicapra) - Almost every Javan zoo and Bali Safari & Marine Park * Nilgai (Boselaphus tragocamelus) - Almost every Javan zoo and Bali Safari & Marine Park * Mishmi takin (Budorcas taxicolor taxicolor) - Taman Safari Bogor * Striped hyena (Hyaena hyaena) - Batu Secret Zoo and Bali Safari & Marine Park * Fishing cat (Prionailurus viverrinus) - Gembira Loka Zoo * Mainland clouded leopard (Neofelis nebulosa) - Batu Secret Zoo * Snow leopard (Panthera uncia) - Jihlava Zoo will sent a second snow leopard to Batu Secret Zoo in the future, Taman Safari Bogor formerly houses a couple * Bengal tiger (Panthera tigris tigris) - Almost every Indonesian zoo * Himalayan black bear (Ursus thibetanus laniger) - Taman Safari Prigen and Bali Safari & Marine Park * Indian rhinoceros (Rhinoceros unicornis) - Batu Secret Zoo Formerly: * Denison barb (Sahyadria denisonii) - Jakarta Aquarium and Taman Mini Indonesia Indah * Dwarf gourami (Trichogaster lalius) - Jakarta Aquarium * Sun catfish (Horabagrus brachysoma) - Taman Mini Indonesia Indah * Goonch (Bagarius yarrelli) - Taman Mini Indonesia Indah * Common crane (Grus grus) - Taman Safari Bogor * Lion-tailed macaque (Macaca silenus) - Batu Secret Zoo * Markhor (Capra falconeri) - Batu Secret Zoo and Taman Safari Prigen * Indian sloth bear (Melursus ursinus ursinus) - Ragunan Zoo Privately keep: * Yoyo loach (Botia almorhae) * Zebrafish (Danio rerio) * Honey gourami (Trichogaster chuna) * Canara pearlspot (Etroplus canarensis) * Dwarf goonch (Bagarius bagarius) * Rainbow snakehead (Channa bleheri) * Channa stiktos * Malabar snakehead (Channa diplogramma) * Barca snakehead (Channa barca) * Indian roofed turtle (Pangshura tecta) * Indian tent turtle (Pangshura tentoria) * Tricarinate hill turtle (Melanochelys tricarinata) * Black pond turtle (Geoclemys hamiltonii) * Indian flapshell turtle (Lissemys punctata) * Elongated tortoise (Indotestudo elongata) * Monocled cobra (Naja kaouthia) * Bengal monitor (Varanus bengalensis) * Plum-headed parakeet (Psittacula cyanocephala) * Alexandrine parakeet (Psittacula eupatria) * Gray peacock-pheasant (Polyplectron bicalcaratum) * Ruddy shelduck (Tadorna ferruginea) * Pallas's cat (Otocolobus manul) Ragunan Zoo labelled their large softshell turtle as a "Indian narrow-headed softshell turtle (Chitra indica)", but I think it's just a mislabelled Javanese narrow-headed softshell turtle (Chitra chitra javanensis). I can only find one picture of the individual: REPUBLIC OF GIS: Visiting Chitra-chitra (Asian narrow-headed softshell turtle) in Ragunan zoo, Jakarta Let me know if I missed any species or zoos/aquarium that currently/formerly keep the species.
My last visit is in around 26th of December, and I remember seeing them in there though, in the Reptile Garden, I believe. The wikipedia also still lists the Indian Star Tortoise there.