Bullet trains running between the two western Japan cities of Osaka and Hiroshima will suspend operations Sunday morning in anticipation of heavy rain and wind, operator West Japan Railway said on Saturday.
Many flights were canceled at major airports throughout Japan, including Tokyo's Narita and Haneda.
Trami was expected to hit Tokyo late Sunday, and slam northern Japan on Monday.
Greater Tokyo is the world's largest metropolis, with a population of about 36 million people.
A powerful typhoon was ripping through Japan on Sunday and authorities were warning people to brace for heavy winds and rain in areas that include those devastated by a previous storm.
Storm winds shake a tree in the Okinawa prefectural capital of Naha, on September 29, 2018, as the powerful Typhoon Trami approaches. Several houses were flooded or damaged and 40 people on the island sustained minor injuries but no one was feared dead, local officials said.
"We are strongly urging our residents to stay indoors because it is extremely risky to be outside now", said Masaaki Tamaki, an official of Kagoshima's disaster management section.
Precipitation over the 24-hour period ending 6 a.m. on September 30 is estimated at up to 400 millimeters in the Amami Islands, 350 millimeters in southern Kyushu, 300 millimeters in Okinawa, 250 millimeters in northern Kyushu, 200 millimeters in Shikoku and Tokai, 150 millimeters in Kinki, 120 millimeters in Kanto-Koshin, and 100 millimeters in the Chugoku region of western Japan.
The agency said the kind of heavy rain only seen once in half a century has been monitored on the island of Yakushima, in the southern part of Kagoshima Prefecture.
Over Sept. 29 to 30, the typhoon is expected lash the Amami Islands, Okinawa, Southern Kyushu, Shikoku and Kinki in southwestern and western Japan with strong winds of up to 50 m/s (180 kph), with maximum gusts hitting 70 m/s (252 kph) in the Amami Islands. "That woke me up", a local elderly man in Kochi told national broadcaster NHK.
The typhoon is projected to hit regions ravaged earlier this month by Typhoon Jebi, which caused landslides and floods and temporarily shuttered Kansai International Airport.
Even for a nation accustomed to disasters, this year has been hard for Japan, starting with a volcanic eruption in January that rained rocks down on a ski resort, killing one.
Also in September, a magnitude 6.6 quake rocked Hokkaido, setting off landslides and leaving more than 40 people dead.