The structures maybe the ruins of a 5,000-year-old city that featured a castle, several temples, and a stadium, according to a Japanese researcher who has been diving at the site for past 15 years.
"The largest structure looks like a complicated, monolithic, stepped pyramid that rises from a depth of 25 meters [82 feet]," said the scientist, Masaaki Kimura of the University of the Ryukyus. Kimura recently suggested that the site might have been sunk by a massive tsunami similar to the one that hit the island in 1771.
But other experts who have dived at the site, which was discovered in 1986, are equally convinced that the formations are natural.
"It's basic geology and classic stratigraphy for sandstones, which tend to break along planes and give you these very straight edges," said Robert Schoch, a professor of science and mathematics at Boston University and a leading critic of the theory.
A natural cliff face on Japan's Yonaguni Jima resembles the "steps" of the mysterious stone structures that lie off the island's coast.
Experts like the University of Boston's Robert Schoch believe that the formations are interesting but completely natural.
"The first time I dived there, I knew it was not artificial," Schoch said. "It's not as regular as many people claim, and the right angles and symmetry don't add up in many places."
But Masaaki Kimura, proponent of the sunken-city theory, is undeterred.
"The best way to get a definitive answer about their origins," he said, "is to keep going back and collecting more evidence."