Rescuers found the three men dead on a popular mountain trail at an elevation of nearly 3,000 meters connecting two mountains, Mt Hinokio and Mt Hoken, Nagano prefectural police official Akira Ito said.
The area is part of a mountain range known as the Central Alps.
The three as well as the missing man are part of a group of 20 South Korean amateur climbers aged between their 40s and 70s.
The cause of their deaths was not immediately known, although Ito cited an illness or hypothermia as a possibility.
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The group began climbing Sunday without a Japanese guide and sought help after nine of them were separated from the group amid a rain storm and thick fog that hit the area Monday. All but the four have been confirmed safe.
The area is not a place for picnicking and requires full preparation and physical strength, Ito said. Police interviews with some of the group's survivors have not revealed any obvious problems in their preparations, he said.
In 2009, eight Japanese senior citizens died of hypothermia after being hit by a rain storm while climbing a mountain in Hokkaido in the north of the country. That case exposed the risks of mountain climbing as a growing trend among senior citizens in Japan as a way to stay healthy.