The New Year's rush began Friday, with vacationers mobbing airports, railroad stations and highways.
The number of travelers during the holiday period is expected to rebound from below average figures last year, which was clouded by Y2K computer problem fears.
Six Japan Railway companies said the number of reservations rose on a year-on-year basis for the first time in four years.
The outflow of trains from urban centers is expected to peak today. The rush back will culminate Wednesday, according to the six railways.
Bullet trains leaving Tokyo had high seat occupancy rates all day, and aisles in cars with non-reserved seats were filled with standing passengers, JR officials said.
The Hikari express No. 161 bound for Okayama marked the day's highest occupancy rate, 130 percent, while most trains on Tohoku shinkansen heading for northeastern Japan also enjoyed occupancy rates above 100 percent, they said.
Meanwhile, most airliners leaving Tokyo's Haneda airport were fully booked, leaving many people waiting in long lines inside the airport, hoping for ticket cancellations.
The airlines said flights from Tokyo were almost fully booked through today, while return passengers will likely be concentrated on Wednesday and Thursday.
Meanwhile, a record number of reservations have been made for international flights over this New Year's holiday.
Highways are unlikely to experience the same 50-km-long traffic jams as last year, according to the Japan Road Traffic Information Center.
Tomei Expressway set Friday's record for the longest traffic jam of the day at 24 km near Miyoshi interchange in Aichi Prefecture. Highway congestion should be 20 km to 30 km long at most, with the heaviest traffic occurring today and Sunday, it said.