South Korea fired warning shots at one of the North's patrol boats as it strayed across the border, Seoul's defence ministry said, raising tensions while a rare reunion for families separated by the peninsula's 1950-53 war was underway.

The South's navy were launching a crackdown on Chinese fishing boats illegally operating off the country's western coast Saturday when it spotted the patrol vessel and fired five warning shots.

The North Korean ship returned across the border soon afterwards without firing back, the defense ministry added.

But Pyongyang on Sunday described the incident as a "serious military provocation" and accused Seoul of seeking to reverse recent improvement in ties.

"The shelling that was committed in broad daylight was a deliberate provocation to spark off a military conflict...and again escalate the tension on the Korean Peninsula," the Committee for the Peaceful Reunification of Korea, which handles cross-border affairs, said in a statement.

"The recent military provocation of the South Korean military gangsters was a dangerous act aimed to chill the hard-won atmosphere of improving the relations and totally derail the process for implementing the North-South agreement," the statement said.

In August the two Koreas agreed to work together to defuse military tension and hold another temporary reunion for families separated by the Korean War.

The October 20-26 reunion -- only the second in five years -- is currently underway in the North's Mount Kumgang resort, with hundreds of people meeting their families for the first time in nearly 70 years.

North Korean incursions over the Yellow Sea border -- which Pyongyang does not officially recognise -- are not unusual.

The border -- drawn unilaterally by the US-led United Nations forces after the war -- was the scene of brief but bloody naval clashes in 1999, 2002 and 2009.