Japan was on alert for typhoon winds and heavy rain Saturday as the death toll from a devastating hurricane that hit the country's north earlier this week rose to 15.

Typhoon Namtheun was heading north towards the southern main island of Kyushu with gusts of up to 198 kilometres (123 miles) 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.

Meanwhile, the death toll from typhoon Lionrock in northern Japan rose to 15 after the body of a 57-year-old man was found in Iwaizumi, Iwate prefecture, police and local government officials said.

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.

Some 1,000 people were still cut off in isolated communities in Iwate prefecture, the prefectural government official said.

"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.