Rescue workers had been searching three people -- a man in his 90s, a woman in her 80s, and a man in his 40s -- who were living in a wooden house that collapsed after the landslide in Matsuyama, Ehime prefecture.
The landside occurred early Friday morning as the weather agency warned of heavy rain in western Japan, with officials calling on people to be on high alert for landslides and flooding in low-lying areas.
Two men and a woman were confirmed dead after a search that continued through the night, an Ehime official told AFP.
"We still don't know if the three who were discovered are those who have been unaccounted for," he said, noting that officials were trying to verify their identities.
Japan is currently in its annual rainy season, which often brings heavy downpours, and sometimes results in flooding and landslides as well as casualties.
Scientists say climate change is intensifying the risk of heavy rain in Japan and elsewhere, because a warmer atmosphere holds more water.
The landslide occurred at the foot of a hill where the imposing Matsuyama Castle is located.
As of early Friday morning, Matsuyama had recorded 213 millimetres (8.4 inches) of rainfall since Wednesday, an amount almost equal to the average for the entire month of July, public broadcaster NHK has reported.
After the landslide, the city issued the highest-level evacuation alert for about 22,000 people in more than 13,000 households.
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