"The North Korean boat sailed into the southern side of the sea boundary but retreated after our naval ship fired warning shots," a ministry spokesman told the AFP news agency.
It was not clear whether the incursion was intentional. North Korean patrol ships sometimes sail into southern waters to track Chinese vessels fishing illegally near the sea border.
The two Koreas remain technically at war since the Korean conflict was concluded with a ceasefire rather than a peace treaty, and small border incidents in the past have been known to escalate swiftly.
In November 2010, North Korea shelled a front-line island, killing four South Koreans and briefly triggering concerns of a full-scale conflict.
In March this year, the North threatened to fire on sight without warning at any South Korean naval vessels violating the sea border.
Cross-border tensions have remained high this year due to a series of North Korean ballistic missile tests, nuclear threats and annual US-South Korean military exercises.
Pyongyang sees the joint drills as a rehearsal for invasion. South Korea and the US say they are purely defensive.
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