A South Korean defence ministry official said up to 20 warning shots were fired at North Korean troops who approached too closely to the "military demarcation line", apparently in search of the missing soldier.
Thursday's defection came about five weeks after another North Korean soldier suffered critical gunshot wounds during a defection dash across the border on Nov. 13.
Two North Korean civilians who were found in a fishing boat on Wednesday had also sought to defect, officials in the South said.
That brings the total number of North Koreans who have defected by taking dangerous routes either directly across the border or by sea to 15 so far this year, including two other soldiers. That is three times the number last year, according to South Korean officials.
Tensions on the Korean peninsula were already high after North Korea accelerated testing of its missile and nuclear programmes this year in defiance of international pressure.
The rash of defections also threatens to complicate South Korea's efforts to ensure the smooth running of the 2018 Winter Olympics, which begin in Pyeongchang in February.
South Korean President Moon Jae-in said on Tuesday he had proposed postponing major military drills with the United States until after the games in an attempt to soothe relations, although officials in Seoul later said any proposed delay would depend on the North not engaging in any "provocations".
Seoul says more than 880 North Koreans have defected to the South so far in 2017, but the vast majority have taken a less dangerous route through China.
Going through China, North Korea's neighbour and sole major ally, means they avoid the heavily fortified demilitarised zone, which features landmines, barbed wire, surveillance cameras, electric fencing, and thousands of armed troops on both sides.
The number of defectors arriving successfully in the South has dropped since North Korean leader Kim Jong Un took power in late 2011, a trend defectors and experts say may be linked to a crackdown by Pyongyang.
There was no immediate comment from the secretive North about the latest incidents.
However, the North's state media released a statement sharply denying U.S. allegations this week that Pyongyang was behind a number of recent cyber attacks.
Washington has publicly blamed North Korean hackers for a cyber attack in May that crippled hospitals, banks and other companies. Researchers also say the North was likely behind attacks on virtual currency exchanges.
The military drills with the United States have also complicated relations with China. South Korea says it needs the drills to guard against the North's missile and nuclear ambitions but Pyongyang describes them as preparation for war.
The proposed delay in drills was discussed during a summit between Moon and Chinese President Xi Jinping last week after the proposal was submitted to Washington, an official at the presidential Blue House said this week.
Beijing was angered when the South deployed a controversial U.S. anti-missile system this year. China fears the system's powerful radar can see far into its territory and the row led to China taking economic measures that included blocking tour groups from visiting South Korea.
Some blocks on group tours had resumed, industry sources said this week, and Beijing has also rebuked Seoul for firing warning shots at Chinese fishing boats.
Defection In Heavy Fog
In Thursday's defection, a low-ranking soldier crossed the border near a South Korean guard post in the "centre-west" region at around 8:04 a.m. (2304 GMT Wednesday), South Korea's Joint Chiefs of Staff spokesman Roh Jae-cheon said. No shots were fired at the soldier.
Surveillance equipment detected him despite heavy fog that limited visibility to about 100 metres (110 yards), Roh said.
"Our military secured his safety, and a questioning will be conducted by related agencies to find out the background of his defection and motive, etc," he said.
South Korean guards fired about 20 warning shots at North Korean troops near the border presumably searching for the defector about half an hour later, a defence ministry official in the South told Reuters.
Gunfire from the North was detected later but the target could not be determined, the official said.
The United Nations Command, which maintains military forces along the border in the South, said it was aware of the incident and was coordinating with the South Korean military to determine the circumstances of the defection.
South Korea's Unification Ministry also said maritime police had found two North Korean men drifting in a small boat off the coast on Wednesday. The pair "expressed their willingness to defect", a ministry official said, and their claim for asylum was being investigated.
The North Korean soldier who was shot several times during a daring dash across the border on Nov. 13 has since been identified as 24-year-old Oh Chong Song and is now in a military hospital south of Seoul.
His treatment for gunshot wounds and pre-existing conditions has included two major operations and intelligence officials will begin questioning him soon.
(Additional reporting by Hyonhee Shin and Heekyong Yang in Seoul)
(This story has not been edited by NDTV staff and is auto-generated from a syndicated feed.)