The Joint Chiefs of Staff said the boat and its crew were "presumed to have defected" from the isolated, nuclear-armed North.
The vessel was intercepted in waters off the eastern port city of Sokcho and those aboard brought to safety, it added.
The boat was carrying four North Koreans who "expressed their intent to defect", Yonhap News Agency reported, citing an unnamed government source.
More than 30,000 North Koreans have fled to the South over the decades since the 1950-53 conflict to escape repression and poverty.
But numbers plummeted to just 67 last year, after Pyongyang imposed a strict border closure to protect itself from the coronavirus that first emerged in its neighbour and key ally China.
Only a handful of Northern defectors have ever directly crossed the de-facto maritime border, or the demilitarised zone that divides the two countries, which remain technically at war.
The vast majority of defectors first travel to China, sometimes staying there for years before making their way on to the South via third countries.
But the route across the northern land border is just as risky, with escapees often facing arrest and possible deportation back to North Korea if they are caught.
Activists say the fugitives face severe punishment, or even a death sentence if forced to return home.
This month, Seoul's unification ministry said a large number of North Koreans appeared to have been repatriated from China.
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