Five shots were fired at 15:30 on October 24 when the patrol boat crossed the de facto maritime border, Yonhap said.
North Korea disputes the maritime border in the Yellow Sea and has crossed it before.
Pyongyang called the shooting a “serious provocation”.
According to North Korea’s official KCNA news agency, the boat was conducting a “routine” operation.
The line was breached several times in February 2014.
Ships between North and South Korea briefly exchanged fire near Yeonpyeong island last October.
The incident comes as the two Koreas hold the second of two reunions for family members separated by the Korean War.
The family reunions taking place this week are only the second round in the past five years.
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