The bodies of a 93-year-old man, his 88-year-old wife and their son, 61, were found near their house in remote Senboku, Akita prefecture, local police said.
Nearly 300 police and troops were still looking for the son's wife, an Akita police spokesman said.
Their home was among eight buildings swallowed by a mudslide triggered by torrential rain that swept the region yesterday, the spokesman said.
Rescue workers also found the body of a 58-year-old in the rubble in the same area.
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The rainfall caused mudslides and rivers to overflow in Akita and neighbouring Iwate prefecture.
Yesterday, rescue workers in Iwate found the body of a 91-year-old woman, whose house in Hanamaki city was also hit by a mudslide.
The Iwate police yesterday also found the body of a 62-year-old man who is believed to have drowned after being swept away by an overflowing river.