I had taken a diving tour at Yonaguni this year. The explanation by the diving instructor was the structure was carved out of stones and foundations, but they were drowned by rising sea levels thousands of years ago. A intermediate level of diving experience can get you there. There are some diving shops that offer this tour on Okinawa island. And the waters there are of high clarity. Would highly recommend this diving tour to anybody who visits Okinawa for vacation!