National broadcaster NHK warned that high-speed winds could fell power lines and damage homes, while heavy rains could trigger flooding and landslides.
The Central Japan Railway company has announced that it will cancel or suspend around 50 bullet train services between Tokyo and Osaka and several Japan Airlines flights across the region have been cancelled.
A powerful typhoon in Japan has left more than 100 flights canceled, thousands of travelers stranded at the airport, and almost 1 million households without power. The storm brought 17 inches of rain to the city of Izu in Shizuoka prefecture in 24 hours through early Monday, with more than four inches falling in an hour.
Almost 290,000 households lost power in the region, while at least 10 houses were damaged in Shizuoka with windows shattered and cars flipped onto their sides, according to local media.
A powerful typhoon is forecast to make landfall near Tokyo late Sunday, packing winds of up to 134 miles per hour and the threat of heavy rain as more than 100,000 people have been told to evacuate.
A 79-year-old New Zealand woman who came to Japan with her husband for the first time said it was "stressful" being stuck at JR Tokyo Station for hours without being unable to understand what was happening.
A separate typhoon struck the Korean Peninsula over the weekend, killing three people in South Korea and five in North Korea, according to local media reports.
The storm comes as Japan prepares to host the Rugby World Cup, which is expected to draw more than 400,000 overseas visitors.
The typhoon also damaged rail lines, including a tree fall on a line linking Tokyo to the southern suburbs, towards Yokohama.
The strong winds downed trees and power lines, with left 910,000 people without electricity in the Tokyo area on Monday morning, NHK said.
The Australian team's arrival was delayed by the storm.
There are concerns the latest typhoon could worsen severe food shortages in the country.
But following close on the heels of the storm forecasters say temperatures are due to soar.