Dujuan had sustained winds of 130km/h (80.8mph) and gusts of 194 km/h.
The typhoon is the latest in a series of storms in the Pacific, made more intense by the "super El Niño", which has warmed the ocean, fuelling the formation of storms.
Authorities had advised the public to pay attention to weather information.
Dujuan, which is Japan's 25th typhoon of the year, hit in the midst of a five-day holiday and forced the cancellation of several events.
Concerts scheduled for Monday at the Rock in Japan music festival were cancelled, while the Tokyo Game Show, a video game convention, also cancelled Monday's programme.
Japan's Prime Minister Sanae Takaichi offered her condolences in a post on X to those who lost thier lives in the typhoon, before saying she would be continuing with her scheduled trip the United States as planned.
"With a sense of urgency, I instructed Chief Cabinet Secretary Takehara and Minister Hosono to respond with utmost preparedness," she wrote, before saying she had boarded a flight to the US.
She will be speaking at the UN General Assembly in New York on Tuesday, and will meet with US President Donald Trump.