The military has come under fire for engaging in a 43-hour standoff with a conscript who went on the run after killing five soldiers and injuring nine others at a border outpost on Saturday.
The soldier, identified as Lim, was captured on Monday after a botched suicide attempt.
Defense Ministry spokesman Kim Min-seok told reporters Monday one person was accidentally shot in the process of apprehending Lim and taken to hospital. The victim was a corporal who was grazed in the temple by a bullet. He was airlifted to hospital and is in stable condition.
The accidental shooting occurred some distance away from where troops had cornered Lim and appears to be the result of soldiers mistaking each other for the runaway sergeant due to a lack of tactical communication between units.
"The accidental discharge appears to have occurred as troops closed in on Lim and tensions were high," the ministry spokesman said.
The military issued its highest alert two hours after Lim had gone AWOL, twice as long as it usually takes. The military is required to conduct joint operations with police under such circumstances, but civilian law enforcement authorities were kept in the dark.
Police in Goseong learned about the shooting on the news and had to call the military for confirmation.
Lim was finally captured on a mountain 10 km from the scene of his crime. Some 43 hours had passed since he threw a grenade and fired more than a dozen shots with his K-2 rifle at his comrades before fleeing the scene.
The Army has come under fire for failing to move quickly to block Lim's escape routes. He engaged his pursuers in several shootouts from the early hours of Sunday.
More than 500 residents in nearby villages hunkered down in fear after hearing the gunshots, but it was not until late Sunday afternoon that they were evacuated to a nearby school.