North Korea has accused the South of committing a "grave military provocation" by allowing its navy to fire warning shots to ward off vessels from the North.
In a communiqué published by Pyongyang's official Korean Central News Agency (KCNA), North Korea said Seoul's military action may give rise to another skirmish at sea.
North Korea said its ships were on routine patrol in North Korean waters when the warning shots were fired.
South Korea says the shots were fired after North Korean ships crossed a disputed maritime border in the Yellow Sea.
South Korean officials say in two separate incidents Monday North Korean vessels ignored radio warning messages and returned to their country's waters only after shots were fired. The North Korean ships did not fire.