The death toll from a typhoon that pounded Japan this week has risen to six, while five other people including two US serviceman remain missing, reports said Tuesday.

Powerful typhoon Phanfone whirled over Tokyo and other major cities during the Monday morning rush hour, cancelling some 600 flights and suspending more than 100 bullet train services while many factories were shuttered.

The storm, which left a trail of damage across the archipelago, was downgraded to a low-pressure system by Monday night as its eye moved out over the Pacific Ocean, Japan's meteorological agency said.

Among the dead was a US military official who had been photographing the storm along with two still-missing colleagues who were engulfed by high waves triggered by the typhoon on the southern Okinawa island chain, local police said.

In Yokohama, southwest of Tokyo, two men in their 20s and 30s were killed separately as landslides destroyed their homes, a city official said.

The Asahi newspaper said the typhoon left a total of six people dead and five others missing, mainly in central and eastern Japan.

About 62 people were injured across the country in storm-related accidents, public broadcaster NHK reported.

Japan's National Police Agency has not yet announced an official death toll, while local authorities were still investigating deaths that might have been caused by the huge storm.

Heavy rains also forced rescuers to suspend the search for victims of the September 27 eruption of Mount Ontake in central Japan, where 12 people remain missing.

Two more bodies were found near the volcano's summit Tuesday morning as the recovery operation resumed following the eruption, which is known to have killed 51 others.

The weather agency has warned that even as the storm passed out to sea landslides and floods were still a risk in a country where a relatively wet summer brought numerous landslides, including in Hiroshima, where more than 70 people died.

In the central Japanese prefecture of Shizuoka, more than 50,000 people were ordered to evacuate their homes, while around 1.7 million others were advised to take refuge, local authorities said.