With thousands of people heading off for their summer vacations on Saturday, many places, such as railway stations, expressways and airports, were crowded with travelers.
The annual Bon holiday season began the same day.
Many shinkansen bullet trains reached over 100 percent occupancy in unreserved carriages, and traffic jams stretching for more than 30 kilometers (18 miles) were seen on some expressways.
According to railway operators, passenger capacity in unreserved seating carriages on the Tohoku Shinkansen Line from Tokyo to the northeastern city of Morioka reached 150 percent in the morning, while the shinkansen from Nagoya to Hakata saw an occupancy rate of 180 percent.
A section of the Sanyo Expressway in Okayama Prefecture was backed up for 40 km (about 25 miles), while other areas on expressways in western, central and eastern Japan saw traffic jams longer than 20 km (12 miles), according to the Japan Road Traffic Information Center.
On the Shin Tomei Expressway in Shizuoka Prefecture, a truck rammed into a line of cars stuck in traffic at around 6 a.m., killing one person and injuring six others, and causing the section of the expressway in Numazu to be closed for over four hours.
The holiday exodus also led to congestion at airports.
Airlines said travelers' departures on international flights would peak between Friday and Saturday, while those on domestic flights will continue through Monday.
The rush of people returning from their vacations by bullet train and on expressways is expected to peak Thursday.