The soldier claimed he shot dead his platoon and squad chiefs while on guard duty at a North Korean picket facility near the Demilitarised Zone shortly before crossing the border yesterday, the JCS said.
South Korean border guards took the soldier into custody and are currently questioning him, it added.
Defections across the DMZ, especially by a North Korean soldier who killed his superiors before fleeing, are rare.
The last defection by a North Korean soldier across the zone reportedly occurred in March 2010.
The South Korean guards heard six gunshots just before the North Korean soldier crossed the border unarmed, telling them he was defecting to South Korea.
They also saw two men being carried out of the North's facility, according to the South Korean forces.
No unusual military movement has been detected so far from the North Korean side of the border after the crossing, but the South Korean forces immediately ordered border troops to step up their guard, they added.
The North Korean facility, which is in charge of inspecting South Koreans entering the country, is only 500 meters away from the South's similar facility.
The area where yesterday's defection took place is along the route to an industrial complex financed by South Korea in the North Korean border town of Kaesong.
The two Koreas are technically still at war since the 1950-53 Korean War ended with a cease-fire, instead of a peace treaty.
Seoul: A North Korean soldier defected to South Korea across the heavily armed border between the two countries after killing two of his superiors, the South's Joint Chiefs of Staff said.
First Published: Sunday, October 07, 2012, 15:52