Six fishing boats from the North violated the maritime boundary, known as the Northern Limit Line, since 11 a.m., Yonhap news agency reported.
South Korean navy vessels broadcasted radio warnings and fired dozens of warning shots before the North Korean boats returned to north of the sea border around 4 p.m.
North Korean ships north of the NLL didn't return fire, officials said.
"Our military is closely monitoring to figure out the intention of the North Korean boats' border crossings," an official said, asking anonymity due to the sensitivity of the issue. "If North Korean boats repeatedly cross the NLL for fishing, the military will promptly and sternly respond, without hesitation."
North and South Korea have occasional clashes at sea, CNN reported.
Those skirmishes have sometimes been fatal, as in 1999, 2002 and 2009. In 2010, the South accused the North of sinking one of its vessels, killing 46 South Korean sailors. North Korea has repeatedly denied the allegations.