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The wounded soldier was evacuated from the site for emergency medical attention, the statement said, after defecting from a North Korean guard post at the Joint Security Area on the heavily-guarded border between the two countries.
The soldier is reported to have left the North Korean guard post in front of Panmungak, on the border inside the demilitarized zone, or the DMZ, and proceeded to move towards Freedom House on the South Korean side.
The UN Command in South Korea said the person drove a vehicle near the military demarcation line, the de facto border between the countries.
"He then exited the vehicle and continued fleeing south across the line as he was fired upon by other soldiers from North Korea," the command said.
The man "initially took cover near a building on the southern side" of the Joint Security Area. South Korean and US forces took him to the Ajou University Medical Center.
At a South Korean Ministry of Defense press briefing on Tuesday, a spokesman confirmed the fleeing North Korean had been hit in the elbow and the shoulder.
The spokesman said the defector's vehicle had gotten stuck in a gutter close to the border, after which he jumped out of the vehicle and ran towards the South Korean side.
According to the ministry spokesman, South Korean soldiers did not return fire. It's still unclear under what conditions the North Korean defector was retrieved, with the spokesman saying he was found collapsed in some bushes.
The command's Military Armistice Commission notified the North Korean People's Army that "the individual is being medically treated at this time and an investigation into the incident is underway."
The Ministry of Defense confirmed to CNN more than 40 bullets were fired at the defector during his escape to South Korea, five of which hit him.
Some were pistol rounds while others were from an AK-47, the ministry spokesman said. There has been no confirmation yet whether the bullets crossed into South Korea.
The soldier was still in a critical condition in a South Korean intensive care unit at Ajou University Hospital, a spokesperson confirmed to media on Tuesday.
DMZ defections
Monday's defection is the third by a member of the North Korean military this year, following two soldiers who fled to South Korea separately in June.
Prior to 2017, there had only been four military defectors from North Korea over the past five years: one in 2016, one in 2015 and two in 2012.
Robert Kelly, associate professor at the Department of Political Science at Pusan National University, said the prominent defection and the shooting was "genuinely surprising."
"It's fairly unusual, I can't think of the last time (a defector was shot at) ... it certainly adds to the tensions," he said.
The defector is currently in South Korean military custody, according to the statement.
"Our military has raised the alert level in anticipation of North Korean provocation. The military is maintaining a full readiness," the Joint Chiefs of Staff statement said.
US man arrested
In a bizarre twist, Monday's successful defection from North Korea came as an American man was arrested in South Korea apparently attempting to go in the other direction.
According to South Korea's Ministry of Defense, a 58-year-old man from Louisiana entered a controlled area in Yeoncheon County, on the border with North Korea, early Monday morning.
The man was reported to police by local residents and arrested. Officials said the country's intelligence services, police and military were investigating the case.
South Korea's National Intelligence Service (NIS) confirmed a US citizen had attempted to enter North Korea via the DMZ, but would not give any further information.
CNN's Jake Kwon, James Griffiths and Joe Sterling contributed reporting.