"The South Korean Government wants to clarify again that both countries [Japan and South Korea] should continue to expand bilateral ties on the base of mutual trust, regardless of any emerging problematic issues," the ministry said in a statement.
South Korea deeply regrets the recent actions of Japan with regard to "comfort women" statue in Busan, the ministry added.
Earlier on Friday, Japan decided to recall its ambassador from South Korea when the new statue, dedicated to "comfort women" was placed by activists in front of the Consulate General of Japan in the city of Busan.
Another statue dedicated to "comfort women" was placed in front of the Japanese Embassy in Seoul back in 2011, where it currently remains.
A South Korean non-profit foundation was set up in December 2015 as a result of an agreement between Seoul and Tokyo over the long-standing issue of "comfort women," a term used to describe Korean women forced to work in wartime brothels for the Japanese military during World War II.
Under the deal, the Japanese government poured 1 billion yen (9.61 million dollars) into the South Korean foundation to care for the surviving comfort women and their families.