Amb. Lee Su-hoon also expressed hopes for a visit by Japanese Emperor Akihito to Seoul, which, he said, would contribute significantly to improving relations between the neighboring countries.
The new envoy is to leave for Japan early next week.
"The president seems to be very firm that such historical matters as the comfort women issue should not hamper the important objective of fostering future-oriented relations between South Korea and Japan," Lee told reporters. "(In this regard) I plan to take a two-track approach as much as possible."
The relations have stayed chilled over a controversial deal to address the dispute over imperial Japan's mobilization of Korean women into sexual servitude for its troops during World War II.
He said that historical matters should be well managed, while at the same time cooperation and exchanges between the two countries should be pursued in various areas, including the economic and business fields.
"There are many areas that the two can cooperate on with each other," he said.
South Korea and Japan reached a deal in late 2015 to "finally and irreversibly" resolve the comfort women issue. Tokyo gave an apology for its colonial-era atrocities and agreed to contribute 1 billion yen (US$8.9 million) to a foundation dedicated to supporting the victims.
The deal has been regarded here as lacking Japan's recognition of its government's responsibility and failing to secure consent from Korean victims and public.
The Moon Jae-in administration, which took office in May, is currently reviewing whether the previous government proceeded with the agreement properly. Japan says that both countries have to faithfully enforce what was agreed upon by their governments.
According to historians, more than 200,000 women, mostly Koreans, were coerced into sexual servitude in front-line Japanese brothels during World War II, when the Korean Peninsula was a Japanese colony. Those sex slaves were euphemistically called "comfort women."
When he received his credentials for the post earlier in the day, the new ambassador said that the president had asked him to deal "in a harmonious way" with such historical matters and put in efforts to build future-oriented relations with Japan.
As a way of tackling the current diplomatic logjam with Japan, he cited a possible visit by Japanese Emperor Akihito to South Korea, saying that it would significantly help improve ties. The emperor has expressed a willingness to visit South Korea.
"(A visit by the Japanese emperor) would make a huge contribution to thawing Korea-Japan relations," he said. "I really hope that it will happen."
"There seem to be various restrictions in reality," he said. "I will make efforts to generate the political environment and mood that will enable (it) to happen." (Yonhap)