He was shot by a North Korean soldier but succeeded in crossing, the JCS added, and has been evacuated for medical treatment.
But this incident marks the first time since the Korean War ended in an armistice in 1953 that shots have been fired through the Joint Security Area, defense minister Song Young-moo told lawmakers in Seoul on Tuesday.
The soldier was injured by gunfire from the North Korean side and has been hospitalized, according to South Korea's military.
He was shot in the shoulder and elbow and was taken to a South Korean hospital, the Defence Ministry said.
An official with the South Korean Joint Chiefs of Staff said the North's border guards fired at least 40 rounds.
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.
More than 30,000 North Koreans have defected to the South since the end of the 1950-53 war, but it's very rare for soldiers to flee across the DMZ, much less the Joint Security Area.
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It was not immediately known how serious the soldier's injuries were or why he made a decision to defect.
The CCL is drawn just below the heavily fortified demilitarised zone (DMZ) which divides South Korea from its rogue northern neighbour.
Col. Roh Jae-cheon, a spokesman for South Korea's Joint Chiefs of Staff, said the military first became aware of the situation around 3:31 p.m.
"The military has raised its alertness against the North Korean military's possible provocations and is maintaining its full readiness posture", the official said.
All channels for dialogue are now cut off between Seoul and Pyongyang after North Korea's relentless development of nuclear weapons and missiles. More than a million mines are believed to be buried inside the zone. South Korean soldiers did not return fire.
The most famous incident was in 1976, when two American army officers were killed by ax-wielding North Korean soldiers.
From there they can seek sanctuary and organise a flight to South Korea, where defectors are given assistance and prepared for life outside the hermit state. The attack prompted Washington to fly nuclear-capable B-52 bombers toward the DMZ in an attempt to intimidate North Korea.