The North did not return fire or take other action, the official said.
North Korea has rejected the so-called Northern Limit Line (NLL), which was drawn up at the end of the Korean War, as the maritime border, insisting on a line further south.
The two Koreas remain technically at war because no peace treaty has been signed after the war, and despite several moves to normalise ties, the peninsula is tensely divided.
A North Korean spokesman said the South fired at its vessel conducting “routine” operation, calling it a “serious provocation,” and warned such action could spark military confrontation and refuel tensions on the Korean peninsula.
“There will be only a war disaster, far from the improvement of the North-South relations, as long as the South Korean military warmongers go reckless,” the unnamed spokesman said in comments carried by the official KCNA news agency.
Naval clashes in the region since 1999 killed dozens of sailors on both sides.
In 2010, a South Korean navy vessel was sunk in a torpedo attack that killed 46 sailors. The South blames the North for the attack but Pyongyang denies any role.
In August, the two sides agreed to work for better ties, ending a tense confrontation at the land border that involved trading of artillery fire. The family reunions were seen as one step in improving ties.