Officials say the soldier knocked on the door of a South Korean barracks near the border last Tuesday and told troops there he was defecting.
The incident has prompted criticism of the military's surveillance capabilities.
President Lee Myung-bak summoned the defense minister Thursday and said those responsible for the failure should be punished.
Officials say the front-line unit also falsely claimed that it had spotted the North Korean on a surveillance camera.
On Saturday, another North Korean soldier defected across the border after killing two superiors. Such crossings are unusual.
The Koreas remain technically at war after their 1950-53 conflict ended in a truce.