Akitaka Saiki, head of the ministry's Asian and Oceanian affairs bureau, will exchange views with South Korea on bilateral ties and North Korean issues, the ministry said in a press release.
The visit will take place as the five members of the disarmament talks other than North Korea have begun a flurry of diplomacy in an effort to bring the defiant communist state back to the table.
The six-nation talks bring together the two Koreas, China, Japan, Russia and the United States.
Saiki is expected to meet Wi Sung Lac, South Korea's special representative for Korean Peninsula peace and security affairs, media reports said.
North Korea pulled out of the process in April in protest at a UN Security Council statement condemning its rocket launch in April, which was suspected to be a disguised missile test.
Pyongyang conducted a second nuclear test in May and declared it would go ahead with a uranium enrichment programme which could produce weapons-grade plutonium.
China's foreign ministry said on Thursday its vice foreign minister Wu Dawei, who chairs the talks, had started a visit the same day to Russia, the United States, Japan and South Korea to discuss the Korean nuclear issue.