| Island | Locality | Description | Size |
| Rondo | Sabang, Aceh Province | Uninhabited except by a lighthouse keeper, located north of Weh Island at, bordering India at one of the entrances to the Malacca Straits. | |
| Sekatung | Natuna Islands, Riau Islands Province | Uninhabited, located at, bordering Vietnam, used as stopover point by Indonesian and foreign fishermen. | 0.3 km² |
| Nipa | Batam, Riau Islands | Uninhabited, bordering Singapore, consists for 80% of dead coral and for 20% of sand which is mainly exported to Singapore. | 60 ha |
| Berhala | Serdang Bedagai, North Sumatra | Situated in the Malacca Straits, bordering Malaysia | 2.5 km² |
| Marore | Sangihe Islands Regency, North Sulawesi | Bordering the Philippines | 214 ha |
| Miangas | Talaud Islands Regency, North Sulawesi | Bordering the Philippines. Situated at, 145 nautical miles from the island of Nanusa, and only 48 miles from the Philippines; 678 inhabitants speaking the Talaud language. The island's currency is the Philippine peso. The Dutch East India Company took control of the island in 1677. In 1891, the Philippines had incorporated Miangas in their territory but accepted the verdict of the Permanent Court of Arbitration in favour of Indonesia. | 3.15 km² |
| Marampit | Talaud Islands Regency, North Sulawesi | Situated at, bordering the Philippines, 1,436 inhabitants | 12 km² |
| Batek | Kupang Regency, East Nusa Tenggara | Called Fatu Sinai by East Timor, bordering the Oecusse District of East Timor. Turtle breeding ground and located on the migratory routes of dolphins | 25 ha |
| Dana | Rote Ndao Regency, East Nusa Tenggara | Situated south of Rote Island at, bordering Australia, uninhabited. | |
| Fani | Raja Ampat Regency, Papua | Bordering Palau, inhabited, situated at, 220 km and 35 hours by boat from the city of Sorong. | 9 km² |
| Fanildo | Biak Numfor Regency, Papua | One of the Mapia Islands, uninhabited, bordering Palau, situated at 280 km from Biak Numfor at | 0.1 km² |
| Bras | Biak Numfor Regency, Papua | One of the Mapia Islands, uninhabited, bordering Palau, situated at 280 km from Biak Numfor, 50,000 inhabitants. | 3.375 km² |
