Police discovered the bodies in the town of Iwaizumi while checking another facility in the flooded neighborhood, said Takehiro Hayashijiri, an official at the Iwate prefecture disaster management division.
The identity of the victims and other details, including the whereabouts of their caretakers, were not known, Hayashijiri said. Japanese public broadcaster NHK said the home was for people with dementia.
NHK also reported that authorities have found two more bodies in another town in Iwate prefecture.
"We're making a government-wide effort to assess the extent of damage," Chief Cabinet Secretary Yoshihide Suga told reporters.
The government sent the Self-Defense Force, Japan's military, to help in the rescue and cleanup effort.
Further north, on the island of Hokkaido, at least two rivers broke through their banks.
The embankments gave way early Wednesday morning, NHK said, quoting Japan's Ministry of Land, Infrastructure and Tourism.
Authorities in the town of Minami-furano reported many people trapped in houses and shelters by flooding from the Sorachi river, NHK said.
It was the first time a typhoon has made landfall in the northern region since 1951, when the Japan Meteorological Agency started keeping records.
The scene of large parts of northern Japan covered with muddy water was a shocking reminder of the major tsunami that struck the same region five years ago.
Iwate prefecture, the hardest-hit by the typhoon, is one of the areas still rebuilding from the March 2011 tsunami and earthquake, which left more than 18,000 people dead along Japan's northeastern coast.
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