The island, named Sandy Island on Google Earth allegedly sits between Australia and New Caledonia in the south Pacific.
"We became suspicious when the navigation charts used by the ship showed a depth of 1400 metres in an area where our scientific maps and Google Earth showed the existence of a large island," Dr Maria Seton, a geologist from the University of Sydney, said.
When the voyage's chief scientist, Seton, and her crew sailed past where the island should be, they found nothing but blue ocean, 'Sydney Morning Herald' reported.
"Somehow this error has propagated through to the world coastline database from which a lot of maps are made," said Seton.
The missing island has regularly appeared in scientific publications since at least 2000.
"Even onboard the ship, the weather maps the captain had showed an island in this location," Seton said.
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Seton had no idea how the island came to be on so many maps, but she is determined to get to the bottom of the mystery, the paper said.
"We all had a good giggle at Google as we sailed through the island, then we started compiling information about the seafloor, which we will send to the relevant authorities so that we can change the world map," Steven Micklethwaite from the University of Western Australia said.
The discovery took place onboard the RV Southern Surveyor, Australia's Marine National Facility research vessel, during a 25-day research trip in the eastern Coral Sea.