"Today, two more people were confirmed dead, with the number of victims now totalling nine," disaster-management spokesman Yuta Hara told AFP.
There were still 22 people unaccounted for, said a spokesman for Shizuoka prefecture, where the town is located.
Dozens of homes were swept away in the disaster that hit on Saturday morning, when a landslide descended in several violent waves.
It came after days of intense downpours in and around Atami, which is about 90 kilometres (55 miles) southwest of Tokyo.
Much of Japan is currently in its rainy season, and many parts of the country are vulnerable to landslides because homes are built on slopes where ground can loosen and collapse suddenly after heavy downpours.
Scientists say climate change is also intensifying Japan's rainy season because a warmer atmosphere holds more water.
Confirming the number of people missing after the disaster has been complicated -- many families have summer homes in Atami but primarily live elsewhere, while elderly residents may have moved to care homes, local media said.
But with several dozen people still unaccounted for, rescue and recovery efforts involving about 1,700 police officers, firefighters, soldiers and coastguard members were continuing.
They have been using shovels and buckets to remove mud from mangled houses and soil from wrecked vehicles in an effort to find survivors or the missing.
Persistent rain in the area has at times forced rescue teams to pull back and suspend operations for fear of further mudslides.
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