Seo said three North Korean troops and one soldier who were on guard opened fire on the escaping soldier, firing around 40 shots.
There has been speculation in both North Korea and the United States that Trump may be feigning unpredictability, emulating former USA president Richard Nixon's "Madman Theory" -whereby enemy countries were tricked into avoiding conflict with the U.S., believing Nixon would be irrational and unpredictable in his response.
About 30,000 North Koreans have defected to South Korea since the end of the Korean War, but most travel through China.
Seo said the North Korean soldier appears to have been shot in five places, adding that he had his first operation on Monday.
The soldier shot and injured by the North Korean side while defecting from a military post in front of Panmungak, the main building managed by North Korea in the Joint Security Area, the JCS said in a statement.
According to the Joint Chiefs of Staff, the defector drove a vehicle into the northern side of the JSA before approaching an area just 10 meters (33 feet) from the Military Demarcation Line (MDL). Jointly controlled by the American-led U.N. Command and North Korea, the DMZ is guarded on both sides by hundreds of thousands of combat-ready troops, razor-wire fences and tank traps.
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"He then exited the vehicle and continued fleeing south across the line as he was sacked upon by other soldiers from North Korea", it said in a statement.
"The military has raised its alertness against the North Korean military's possible provocations and is maintaining its full readiness posture", the official said. It's also a popular stop for tourists and dignitaries, including several USA presidents.
He was taken to hospital with gunshot wounds to his elbow and shoulder, South Korean officials said.
"His organs are extremely damaged. we do not know how long he can hold up", Lee said, describing the soldier's condition as "very serious". His helicopter had to turn back because of bad weather.
It was not immediately known how serious the soldier's injuries were or why he made a decision to defect. In September the North carried out its sixth and largest nuclear test, of what it described as a hydrogen bomb.