A manhunt was last night under way after the incident, with the army private believed to have gone on the run carrying a firearm, ammunition and a grenade.
The exact circumstances of the incident at the remote guard post were not immediately clear, although there was no indication that North Korea was involved.
The shooting took place in Goseong County, a mountainous region that borders the North on the eastern end of the peninsula. The border is one of the most heavily fortified in the world, with tens of thousands of soldiers from both North and South Korea stationed along it.
All able-bodied South Korean men must serve around two years under a conscription system that makes up a military of more than 600,000 troops aimed at deterring aggression by North Korea, which is one of the world's most militarised states.
Incidents involving firearms at South Korean military units are not frequent but have occurred in the past, typically when conscripts who have been under stress opened fire on other unit members or deserted the base carrying weapons.
The border across the peninsula was drawn up at the end of the 1950-53 Korean War. The two Koreas remain technically at war because an armistice and not a peace treaty was signed to end the conflict.
North Korea stations a large portion of its 1.2 million military personnel near the border backed by artillery power. It regularly threatens the South and US forces based in the South with destruction.