The person in question was spotted crossing the barriers to the North on Saturday night. His identity was not disclosed.
“Regarding the border crossing, the authorities presume the person is a North Korean defector and are in the process of verifying related facts," the ministry was quoted as saying in a statement to the Yonhap news agency on Monday.
The defector is reportedly believed to be a man who climbed over fencing in the same area of the common border and entered South Korea in November 2020.
On Sunday, South Korea sent a message to the North at the border crossing by a military communication line.
The incident led to concerns in Seoul, which pledged to tighten border security in late 2020 in an attempt to prevent illegal crossings, according to the agency.