The "low-ranking" soldier was spotted by South Korean soldiers using surveillance equipment as he crossed the midwestern part of the land border in thick fog and made his way to a guard post, a ministry spokesman said.
No shots were fired at the time, he said, but South Korean troops later fired around 20 rounds from a K-3 machine gun to warn off Northern guards who approached the border apparently looking for the man.
The incident came a month after a rare and dramatic defection by a soldier at Panmunjom, the truce village where opposing forces confront each other across a concrete dividing line.
On that occasion the defector drove to the heavily-guarded border at speed and ran across under a hail of bullets from his own side. He was hit at least four times.
Footage showed the badly injured man being pulled to safety by two South Korean soldiers who crawled to reach him just south of the demarcation line.
He has since been recovering in hospital in the South.
Away from Panmunjom, the rest of the 4-kilometre (2.5-mile) -wide DMZ bristles with barbed wire and is littered with minefields, making any crossing extremely hazardous.
Uncertain fate
Thursday's defection was the fourth by a soldier across the DMZ this year.
Two North Korean civilians also defected this week after being found drifting in a rickety engineless boat off South's eastern coast, Yonhap news agency reported, citing the Unification Ministry, which handles relations with the North.
They were spotted by a South Korean surveillance aircraft and picked up by a nearby navy vessel, it said.
The developments bring this year's total for the number of people defecting directly to the South to 15, a Joint Chiefs of Staff tally showed -- three times as many as in 2016.
Around 30,000 North Koreans have fled repression and poverty in their homeland to reach the South over the decades since the end of the 1950-53 Korean War, with 1,418 doing so last year according to Unification Ministry data.
The vast majority go first to China, with which the North shares a long border, and where they face the risk of being repatriated to an uncertain fate if caught. They travel on to the South later, often via another country.
In November's Panmunjom incident, footage showed a North Korean guard briefly crossing the border in hot pursuit before retreating.
The US-led United Nations Command said the North's forces had violated the 1953 ceasefire that ended Korean War hostilities both by physically crossing the line and firing weapons over it.
The North Korean soldier, 24-year-old Oh Chong-Song, underwent multiple operations for his gunshot wounds at Ajou University Hospital in Seoul and was transferred to a military hospital last week, Yonhap said.
He has recovered enough to get to his feet and walk with help, it added, and has written a letter of thanks to the medical staff who treated him.
Oh wants to become a lawyer, said his surgeon Lee Cook-Jong, who gave him a law book.
"He said while in the North, he was unable to study much because of his military duty," Lee was quoted as saying. "I just hope he will become a good citizen, whatever kind of occupation he chooses."
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