United Nations Command (UNC) said the soldier had driven close to the heavily-guarded, military demarcation line in a vehicle.
The defection came at a time of heightened tension over North Korea's nuclear weapons programme, and could escalate animosities between the rival countries.
About 30,000 North Koreans have defected to South Korea since the end of the 1950-53 Korean War, but most travel through China. In such volatile conditions, it is troubling that North Korean guards shot numerous rounds at the soldier trying to defect.
Seo said the North Korean soldier appears to have been shot in five places, adding that he had his first operation on Monday.
Seo said that at around 3:14 p.m. on Monday, the JCS spotted three North Korean soldiers moving south of the Panmungak, or the North's main building in the Joint Security Area.
No tourists were in the Joint Security Area at the time and there was no exchange of gunfire between the two sides.More news: Donald Trump asked China's president to help resolve UCLA basketball player arrests
Over the decades since the peninsula was divided, dozens of North Korean soldiers have fled to the South through the DMZ, which extends for two kilometers either side of the actual borderline. The next 10 days will be crucial for his recovery, Lee was quoted as saying by the Yonhap News Agency.
South Korean military said there was no armed conflict after the incident, but they are "increasing alertness" for a possible provocation from North Korea.
The DMZ is a 2.5-mile wide, 150-mile-long buffer zone lined with barbed wire and dotted with landmines. His helicopter had to turn back because of bad weather.
Violence has broken out in the area in the past.
A doctor treating the soldier - who was airlifted to a hospital for emergency surgery - said he had been shot half-a-dozen times and sustained a serious stomach injury.
Suzanne DiMaggio, a director at the think tank New America, told Politico that North Korean officials are confused by the U.S. president's increasingly "erratic behaviour" and "really want to know what his end game is". In September the North carried out its sixth and largest nuclear test, of what it described as a hydrogen bomb.