Authorities advised thousands living in coastal areas or near rivers to evacuate to shelters as Typhoon Lan, described as "very large and very strong", made landfall in Shizuoka southwest of Tokyo at around 3.00 am (1800 GMT Sunday).
The storm, which had already dumped torrential rain over much of the country during the weekend, packed gusts up to 198 kilometres (123 miles) per hour, the meteorological agency said.
The typhoon was moving northeast as winds slowed slightly, and may hit Tokyo and surrounding regions during Monday morning rush hours.
Train operators in the capital have decided to cancel some express services in the morning, and some "Shinkansen" bullet trains were stalled in central Japan carrying passengers overnight as the typhoon caused a blackout, NHK said.
Nearly 300 flights scheduled for Monday have already been cancelled, the public broadcaster said, after strong winds forced airline companies to ground more than 500 flights Sunday.
Some ferry services in western Japan were also cancelled.
The typhoon claimed its first victims as a male passer-by died when scaffolding collapsed on him at a construction site in Fukuoka, western Japan.
And a 70-year-old man was found dead after he dived into the sea to grab a rope from another vessel as he attempted to escape from his troubled boat, a coastguard told AFP.
At least 11 people were injured across the nation, while a 85-year-old man was unaccounted for after his house was hit by landslides, NHK said.
Television footage showed rescuers tugging a rubber boat carrying an elderly woman in a residential area in Chiba southeast of Tokyo as a flooded river engulfed the area.
Toyota Motor said it would suspend operations at all domestic plants on Monday.
- Emergency response -
Earlier in the day, Prime Minister Shinzo Abe ordered his minister in charge of disasters to be ready to mobilise rescue and evacuation forces, including troops.
"In order to protect people's lives, the Abe cabinet will unite and do its best to provide an emergency response to a disaster," he told reporters.
Several local governments in Osaka and other prefectures issued evacuation advisories, urging thousands of residents living near the coast, rivers and hillsides to move to shelters.
The weather agency separately warned of high waves, landslides and floods in central and western Japan.
Voters in the capital braved torrential rain and driving wind on election day, as a projection from NHK said Abe's ruling conservative coalition was on track to win a two-thirds "super-majority."
Voting was delayed by some 20 minutes in Kochi in western Japan when landslides blocked a road, while several polling stations closed earlier than scheduled.
Ferries to a remote island in the west were cancelled due to high waves, forcing election officials to suspend the counting of votes there.
On Saturday voters on remote southern islands in the path of the storm had cast their ballots early, heeding a call from Abe.
Voter turnout excluding early voting was at record low levels as of 7:30 pm, although some 20 percent of eligible voters cast early votes, the government said.
