Some train and airplane passengers were forced to adjust their plans on Sunday because of Typhoon Hagibis.
The Hokuriku Shinkansen has resumed service between Tokyo and Nagano, but with fewer trains for the time being.
Carriages used on the line were damaged when a storage facility was flooded. The facility in central Japan used to repair or store bullet trains. JR East says water rushed into the facility when the nearby Chikuma River overflowed.
Company officials say 10 trains, a total of 120 carriages, were damaged. That's one third of the trains on the line.
JR East says the Tohoku and Akita Shinkansen bullet trains resumed operations around 4 pm. The restart had been delayed due to rocks and dirt on the tracks.
The Tokaido and Sanyo Shinkansen restarted Sunday morning.
But the Yamagata line will remain out of service for the entire day. JR East says the Yamagata line is expected to be back in service around noon on Monday.
Railway operators in Tokyo and surrounding areas will resume most local train services after they do safety checks.
JR East has resumed service on the Yamanote Line, Tokyo's key loop line. Most of the private railway companies have also restarted operations.
In the resort town of Hakone south of Tokyo, a train line that goes up into the mountains has been closed due to landslides.
Airlines in Japan cancelled more than 800 domestic flights for Sunday.
All Nippon Airways canceled 297 flights, including all flights at Narita airport and some at Haneda. Both airports serve Tokyo.
Japan Airlines also canceled 278 flights, including most departures and arrivals at Haneda and Osaka airports.
Many other airlines have also canceled flights.