The three 17-year-olds, all male, were in the water off Hateruma island in the southern island chain of Okinawa when high waves swept them out to sea, according to coast guard spokesman Shoji Kawabata.
Rescuers found one of the students floating near a coral reef near the island, and he was later pronounced dead at a hospital, Kawabata said. Another was rescued by a local diving boat, while the third remained missing.
There were waves about 3-4 meters (10-13 feet) high in the area due to the typhoon, though the weather was sunny, Kawabata said.
Typhoon Chanchu swept over the Philippines last weekend, killing 37 people and destroying thousands of homes.
It veered to the east and spared Hong Kong on Wednesday before roaring toward mainland China's southern coast, where media reports said over 180,000 people were evacuated.
Hateruma island is about 2,000 kilometers (1,240 miles) southwest of Tokyo and 180 kilometers (112 miles) west of Taiwan.
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