Two bodies were found separately near rivers on the island of Hokkaido, a police spokesman told AFP.
On Thursday evening, police also found a body near a flooded river in the hard hit town of Iwaizumi in the northern part of Honshu island, public broadcaster NHK said.
Typhoon Lionrock, which packed wind gusts of over 160 kilometres an hour landed on Japan's northern Pacific coast on Tuesday evening, dumping torrential rain over a wide area.
Overflowing rivers wreaked havoc, stranding many communities in the country's largely agricultural north.
As of today, more than 1,000 people were still cut off in isolated communities in Iwate prefecture, which includes Iwaizumi, the prefectural government said.
Lionrock was the third typhon to strike Japan's northeast in about 10 days, the previous two causing at least two deaths.
Japan faced another strong typhoon, Namtheun, which was heading north toward the southern main island of Kyushu with gusts of up to 180 kilometres per hour, according to the Japan Meteorological Agency.
In 2013, a powerful typhoon that triggered massive landslides on Oshima island, 120 kilometres (75 miles) south of Tokyo, killed 40 people, while 82 died after a typhoon hit Japan in 2011.
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