Typhoon Namtheun was heading north towards the southern main island of Kyushu with gusts of up to 198 kilometres per hour, according to the Japan Meteorological Agency.
Namtheun was passing near the small subtropical island of Amami, which lies between Okinawa and Kyushu, Saturday afternoon, the agency said.
It issued a warning for strong winds, heavy rain and floods in southern Kyushu, but there was no immediate report of injuries or damage from the typhoon.
Public broadcaster NHK said at least nine people were still unaccounted for.
Lionrock 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.
Iwaizumi was the hardest hit as nine people were buried inside a building of an elderly care facility, which was engulfed by a massive flood from a nearby river.
"We are dispatching helicopters to bring foods and necessary items to the isolated areas," the official said.
Lionrock was the third typhoon to strike Japan's northeast in about 10 days, the previous two causing at least two deaths.
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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