The accusation came amid high tensions sparked by an investigation into the sinking of a South Korean warship near the disputed Yellow Sea border in March.
The North's military made its complaint in a message to the South's armed forces, the Korean Central News Agency reported.
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Over 10 days ending Monday, it said, dozens of the South's naval ships had intruded into the North's waters.
"This is a deliberate provocation aimed to spark off another military conflict in the West (Yellow) Sea of Korea and thus push to a war phase the present North-South relations that reached the lowest ebb," KCNA quoted the message as saying.
If the intrusions continued, the North "will put into force practical military measures to defend its waters as it had already clarified and the South side will be held fully accountable for all the ensuing consequences."
A defence ministry spokesman in Seoul denied any of the South's ships had crossed the border known as the Northern Limit Line.
The North refuses to accept the line drawn by the South's allies after the 1950-53 war and demands it run further to the south.
The area was the scene of deadly naval clashes in 1999 and 2002 and of a firefight last November that left a North Korean patrol boat in flames.
Investigators concluded last week that a North Korean torpedo ripped a South Korean warship in two in the area on March 26, and Seoul Monday announced several punitive measures.
The North has denied responsibility and has threatened "all-out war" if there is any attempt to punish it.
