United Nations Command (UNC) said the soldier had driven close to the heavily-guarded, military demarcation line in a vehicle.
The soldier crossed to the south side of the Joint Security Area at Panmunjom, the only portion of the border Demilitarised Zone where forces from the two sides come face-to-face, the Joint Chiefs of Staff said in a statement.
We are disappointed at the way our military reacted to the shootings on Monday by North Korean guards at a fellow soldier who defected to South Korea through the Joint Security Area (JSA) in Panmunjom.
"In the afternoon today, a North Korean soldier defected from a guard post on the North Korean side of the JSA toward our side and our military took him", the Yonhap news agency quoted an unidentified military official as saying.
He added that South Korean troops did not fire at the North.
An official with the South Korean Joint Chiefs of Staff said the North's border guards fired at least 40 rounds.
The incident, which happened in broad daylight around 4 pm, comes at a time of heightened tensions on the Korean peninsula over the North's nuclear weapons programme.
According to the South Korean military there was no exchange of fire across the border, and the UNC statement stressed that no South Korean or U.S. forces were harmed.
About 30,000 North Koreans have defected to South Korea since the end of the Korean War, but most travel through China.
"The military has raised its alertness against the North Korean military's possible provocations and is maintaining its full readiness posture", the official said.
At Panmunjom, once an obscure farming village inside the 2 1/2-mile-wide DMZ that separating the rivaling countries, North Korean soldiers wearing lapel pins with the images of late North Korean leaders often use binoculars to monitor visitors from the South.
Trump tried to make a surprise visit to the DMZ last week, but his helicopter was forced to turn back to Seoul after heavy fog prevented it from landing at the frontier. In September the North carried out its sixth and largest nuclear test, of what it described as a hydrogen bomb.
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