The South Korean navy has fired warning shots at North Korean fishing vessels that crossed their disputed Yellow Sea border, officials say.

Six North Korean fishing boats crossed the boundary on Friday and refused to return until the South's navy fired the warning shots, an official with South Korea's Joint Chiefs of Staff told the Associated Press.

The official said no North Korean navy ships were involved the incident and the South Korean shots did not hit the fishing boats. Officials said the North Korean boats retreated after the shots were fired.

"Our naval patrol boats twice fired machine gun rounds at the fishing vessels. Afterwards the North Korean vessels retreated to their territory," a South Korean defence ministry spokesperson told the AFP news agency.

The incident was the latest in a series of incursions by North Korean vessels in recent weeks.

North Korean fishing boats already crossed the boundary four times earlier this month but retreated each time after being warned by the South, officials said.

Seoul said North Korean fishing boats also crossed the boundary in April.

Earlier on Friday, South Korea's Yonhap news agency had quoted an unidentified senior military official as saying the navy would take action if the incursions continued.

"If North Korean boats repeatedly cross [the border] for fishing, the military will promptly and sternly respond, without hesitation," the official said.

The de-facto maritime boundary between the two Koreas - the Northern Limit Line - is not recognised by Pyongyang, which argues it was unilaterally drawn by the US-led United Nations forces after the 1950-53 Korean War.

Violence often erupts in the seafood rich waters claimed by both countries. Boats routinely jostle for position during crab-catching season, and three deadly naval clashes since 1999 have taken a few dozen lives.