President Moon Jae-in stressed the need for "constructive and future-oriented" Seoul-Tokyo ties.
He made the remarks during a meeting with Koji Tomita, the outgoing Japanese Ambassador to South Korea.
Moon said the two sides are each other's closest neighbors and important partners that must work together for peace and prosperity in Northeast Asia.
The meeting came after a Seoul court ruled that the Japanese government is to pay over 90-thousand U.S. dollars to 12 Korean victims of Japan's wartime sex slavery.
Tokyo which claims that the issue was settled under a 2015 deal with Seoul, strongly protests the ruling.