The unnamed sergeant crossed the western section of the Demilitarized Zone at 12:06 p.m. Oct. 6, arriving at a South Korean border post 4 minutes later, a report by South Korea's Yonhap news agency said.
South Korean border guards reported gunshots along the border around the same time as the North Korean appeared on the southern side of the DMZ, the JCS said.
He told the South Korean guards on duty that he wanted to defect and handed himself over.
Several of South Korea's security agencies are questioning the North Korean soldier, who said he was on guard duty when he shot his platoon and squad chiefs to death.
Defections are rare across the heavily guarded 2 1/2 mile-wide DMZ, which has been the de facto border since the end of the Korean War ended with a truce, not a peace treaty, in 1953. The two countries technically are still at war.
North Korea's state-run Korean Central News Agency hasn't commented on the incident and alleged killings by the by North Korean soldier.
There are an estimated 1 million soldiers from both sides ranged across DMZ that stretches 160 miles east-west across the Korean Peninsula.
Few people successfully have crossed the border with its million or so land mines and miles of barbed wire. Many take longer but relatively safer land routes through China and on to third countries including Thailand, the BBC said. Many of the defectors remain in China.
The last previous known military defection was by another North Korean sergeant in March 2010, a report by The New York Times said.
The Oct. 6 defection was at a crossing point where South Korean workers enter the North every day to work at an industrial park in Kaesong, close to the border. Products made at the complex, a joint venture between the Koreas, enter the South through the same cross-border road, the Times report said.
One of the first -- and most spectacular -- defections was that of North Korean air force Lieut. No Kum Sok in September 1953. No, 21, landed his MiG-15, then the latest Soviet-made MiG, to Kimpo Air Force Base in South Korea.
He was granted U.S. citizenship and retired in 2000 after working 17 years as an aeronautical engineering professor at the prestigious private Embry-Riddle Aeronautical University, with campuses in Florida and Arizona.
No's Mig-15 underwent extensive flight testing by the U.S. Air Force to gain knowledge of Soviet aircraft design and eventually was sent to the National Museum of the U.S. Air Force in Dayton Ohio, where it remains on display.