At least 51 people were injured in southern Japan, it said, and the Reuters news agency reported one death on Monday.
A 50-year-old truck driver was killed during the storm by a landslide in Tottori Prefecture, and another man was found in a river and later confirmed dead in Yamanashi Prefecture.
A 67-year-old woman, who was dragged through an irrigation channel in southwestern Miyazaki, as well as a 46-year-old security guard in Koka in Shiga Prefecture in central Japan, are missing.
A powerful typhoon pounded Japan's mainland yesterday after injuring dozens on outlying islands, bringing transport grinding to a halt and triggering warnings of fierce winds, torrential rain, landslides and floods. Huge crowds built up at Tokyo train stations, with people battling for spots in jam-packed commuter trains. "I was optimistic that trains would be operating normally in the morning".
East Japan Railway Co.
Strong wind knocked down trees, blew off an outer wall from a building and left nine people injured in Okinawa. Tokyo's train lines announced they were shutting down after 8 p.m. on Sunday.
At a condominium construction site in Shinagawa Ward, Tokyo, the arm of a crane used to hoist construction materials broke, apparently because of the strong winds.
Number of residents nationwide issued with non-compulsory evacuation advisories.
More than a thousand flights were cancelled countrywide and another 249 were called off on Monday, according to NHK.
Some 450,000 households in Tokyo and its vicinity had been hit by power outages as of early Monday. In Nanjo, a gust of 202 kilometres per hour was recorded. It is expected to cross the islands of Kyushu and the main island of Honshu between Sunday and Monday, a path similar to that taken Typhoon Jebi early in September.
"We saw incredible winds and rain".
The JMA has underscored the need to be prepared for disruption of transportation services, power blackouts, and agricultural damage due to the strong winds, heavy rain and high waves. Enormous wind. It was hard to stay standing. "It was very scary", he added.
At its height, Trami packed gusts of 216 kilometers (134 miles) per hour, though it weakened as it moved over land.
In July, heavy rain in western Japan killed 221 people, setting off landslides and flooding.
Typhoon Trami has already sparked travel disruption in the world's third-biggest economy, with bullet train services in the west of Japan suspended and nearly 1,000 flights cancelled due to the closure of a key airport hub.
The number of trains operated on the Hiroshima-Hakata section on the bullet train line will be reduced on September 30. It was the first time that such a planned suspension of train services for the entire Tokyo metropolitan area was implemented.