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Coral cays are low-lying islands formed by coral gravels deposited by the waves and currents on the coral reefs. Cases have also been reported that the coral cays were formed in the short time scales when high waves with storm surges. Once the formation of coral cays can be controlled, which can contribute to the protection, environment and use of the coast on coral reefs and the national land conservation of the Pacific Ocean island nations in danger of inundation by the sea level rise. In this paper, the formation mechanism of the coral cays is verified through hydraulic movable bed model tests and the numerical simulation aimed at Ballast Island in the north of Iriomote Island. As a result, we confirmed that the wave breaking on the reef edge, wave setup, currents, and gravel supplies on the coral reefs exert influence on the formation of coral cays.