Japan is currently in its typhoon season, and faces around 20 such storms a year, routinely with heavy rains that cause flash floods or landslides.
The latest, Talas, was churning near the northeast of the country, 100 kilometres (62 miles) off the coast of Omaezaki at 6 am (2100 GMT Friday), according to the Japan meteorological agency.
It was packing maximum gusts of 90 km per hour, the JMA said.
The agency has issued warnings about high waves, heavy rains, landslides and floods in central, eastern and northern Japan, including Tokyo.
A man in his 40s died after his house was hit by a landslide in Kakegawa, Shizuoka prefecture, local media reported.
In a separate landslide in Hamamatsu, also in Shizuoka prefecture, three people including a nine-year-old boy suffered light injuries, public broadcaster NHK said.
Police could not immediately confirm the reports.
Last weekend, four people were killed and 151 injured after Typhoon Nanmadol slammed into southwestern Japan.
Scientists say climate change is increasing the severity of storms and causing extreme weather such as heat waves, droughts and flash floods to become more frequent and intense.