The soldier said he shot dead two officers before crossing over just after noon on Saturday.
Correspondents say defections across the land border are rare, with the last soldier fleeing in October 2008.
More than 24,000 North Koreans have gone to the South in the last 60 years, mostly via China or SE Asia.
The defence ministry official said the soldier was in protective custody and was still being interrogated.
There has been no confirmation of the North Korean casualties and no unusual activity observed on the North Korean side of the border.
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