Foreign Minister Kang Kyung-wha will hold talks with her Japanese counterpart Taro Kono and meet with Prime Minister Shinzo Abe, the ministry said.
It marked the first trip by a South Korean foreign minister to Japan since June 2015.
The government earlier said that the two ministers will exchange views on issues of mutual concern, including North Korea's nuclear problem and bilateral relations.
The meeting comes as North Korea test-fired a new intercontinental ballistic missile in late November, claiming that it has completed its "state nuclear force."
Relations between Seoul and Tokyo have chilled over a controversial deal reached in 2015 to resolve the long-running feud over Tokyo's wartime sexual slavery of Korean women.
The Moon Jae-in government, which took office in May, has said that the deal reached under its predecessor does not reflect public sentiment and that there appears to be procedural problems.
A task force is currently reviewing how the agreement was reached and expected to provide its assessment on the matter to the government by the end of this month.
Historians estimate that up to 200,000 women, mostly from Korea, were forced into sexual servitude during World War II. Source from the Yonhap.