The bird, Otus jolandae, is only thought to live on the island of Lombok.
Although the owl has been known for at least a century, it has only now been recognised as a new species.
Previously experts had confused it with a more widespread owl with similar plumage.
The bird has a whistling call completely unlike that of other owls.
Two members of an international team independently recorded the signature whistle in 2003.
Ornithologist George Sangster, from the Swedish Museum of Natural History, said: “It was quite a coincidence that two of us identified this new bird species on different parts of the same island, within a few days of being on the island. That is quite a coincidence, especially considering that no-one had noticed anything special about these owls in the previous 100 years.”
Comparisons with museum specimens and previous studies confirmed the discovery and indicated that the owl was confined to one island.
Locals on the neighbouring island of Sumbawa appeared to be unfamiliar with the bird, said Mr Sangster.
“None of the locals recognised the songs from playback of recordings made on Lombok except for one man, but he was an immigrant from Lombok who knew the song,” he said.
The research is published in the online journal Public Library of Science ONE.
The scientists suggest giving the owl the common name Rinjani Scops Owl, after Gunung Rinjani, a volcano on Lombok.