Prince William planned to visit Commonwealth war graves in Yokohama and to attend a trade fair for British products in Tokyo.
The visit is the prince's first trip here and his wife Catherine, who is expecting their second child, is not accompanying him.
The prince will leave Japan Sunday for China through March 4.
The last visit to Japan by the British royal family members was in late 2013 by Prince Andrew. Prince William's father Charles visited Japan in 2008 and his late mother Princess Diana's last visit was in 1995.