The soldier shot his platoon and squad leaders before crossing the western side of the Demilitarized Zone at around noon, a Defense Ministry official said, citing the soldier's statement after he was taken into custody by South Korean border guards.
The official, who declined to be named because questioning by authorities was ongoing, had earlier said one of the killed North Korean troops was a company commander but later corrected it, saying the information was mishandled in the first couple of hours of the development.
He said South Korean guards heard six gunshots before the North Korean soldier crossed the border. He also said the soldier used a loudspeaker to let South Korean guards know his intention to defect after the killings. The official said the motive behind the defection was unclear.
No unusual military movement was detected from the North Korean side of the border after the crossing, but South Korea immediately instructed its border troops to step up their guard, a South Korean Joint Chiefs of Staff official said. He also declined to be named, citing office rules.
There was no immediate comment from communist North Korea's state-run media.
Defections across the land border are rare, though North Koreans occasionally come to the South by boat. Last year, a North Korean civilian defected to the South across the land border. The last defection across the Demilitarized Zone by a North Korean soldier occurred in 2010, officials said. Another soldier and an officer also defected to the South across the border in two separate crossings in 2008.
The vast majority of North Koreans fleeing their homeland travel through China and Southeast Asia before arriving in the South.
More than 24,000 North Koreans have arrived in the South since the 1950-53 Korean War ended in a cease-fire, not a peace treaty.
The area where Saturday's defection took place is along the route to a South Korean-financed industrial complex in the North Korean border town of Kaesong, officials said.
Border security has been tighter than usual along the border in the past few years as military and political tensions between the rival Koreas soared. In 2010, a South Korean naval ship sank and 46 of its sailors died in an incident blamed on North Korea, though Pyongyang denies involvement. Later that year, North Korea bombarded a South Korean front-line island, killing two marines and two civilians.
Associated Press writer Sam Kim contributed to this report from Busan, South Korea.