The North Korea military said via Pyongyang's official news agency that South Korean naval vessels had been spotted in North Korean waters on several occasions this month.
The KCNA statement cautioned that North Korea would "strike without any prior warning at any warship of the South Korean Navy intruding."
Tensions in the area are complicated by Seoul and Pyongyang's difference of opinion on the position of their maritime border -- the recognized Northern Limit Line was decided by the United Nations Command after the Korean War in 1953.
But that conflict never technically ended as the Koreas failed to sign a peace treaty.
In March, the South marked the fifth anniversary of the sinking of its Cheonan warship -- an incident that claimed 46 lives but which the North has denied involvement in.
A separate issue of contention stemming from the border dispute is the protection of fishing rights.