Five East Japan Railway Co. shinkansen lines halted operations for about three hours from the start of service Monday when the control system malfunctioned, affecting about 137,700 holiday travelers and commuters.
The Tohoku, Joetsu, Nagano, Yamagata and Akita Shinkansen lines resumed operations at around 9 a.m.
The problem was caused by a failure in the main system at the bullet-train operations HQ in Tokyo, JR East said.
The shutdown led to 112 train runs being canceled, while 146 other runs operated behind schedule. The failure is believed to have occurred during a system switch-over from midnight Sunday through 6 a.m. A 68-year-old company employee who was planning to return to his wife's hometown in Akita Prefecture said at a crowded Tokyo Station: "I go home this time every year. But this is the first time system trouble has occurred."
At JR Sendai Station, Isao Sugasawa said plans to celebrate his 70th birthday with his family in the hot-spring resort of Hakone, Kanagawa Prefecture, "have been completely ruined" by the disruption.
Bullet train services have been hit by a series of troubles recently, with heavy snow, strong winds and accidents disrupting the Akita, Yamagata, Nagano and Tokaido Shinkansen lines Sunday, affecting more than 30,000 people heading for their hometowns or other holiday destinations.
The Yamagata Shinkansen Line partly halted operations Saturday after a tree fell onto the overhead power lines.