Fossils of the big bird were discovered on the island of Flores, a place previously famed for the discovery of Homo floresiensis, a small hominin species closely related to modern humans, the BBC reported Tuesday.
Discovered in 2004, H. floresiensis is thought to be a human-like species standing just 3 feet tall that survived until about 17,000 years ago.
The new species of stork, named Leptoptilos robustus, reached 6 feet in height and weighed an estimated 36 pounds, researchers say, making it much heavier and taller than living stork species such as the related Marabou stork, which can reach 20 pounds and stand 5 feet tall.
As such it would have towered over the "hobbit" hominins occupying the same island.
Palaeontologist Hanneke Meijer of the Smithsonian National Museum of Natural History in Washington made the discovery with colleague Rokus Due of the National Center for Archaeology in Jakarta, Indonesia.
The fossil bones are between 20,000 to 50,000 years old, they say.
Around 15,000 years ago, the climate of Flores went from dry to being wet, which may have been enough to drive many of the island's species to extinction, the researchers say.
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