While South Korea suffered no casualties, the North Korean vessel returned home "wrapped in flames" after the clash which occurred in South Korean waters off the west coast, Seoul officials said, Yonhap news agency reported.
The incident comes as U.S. President Barack Obama prepares for his scheduled visits to Seoul and other Asian capitals.
It began shortly after a North Korean patrol boat crossed the Northern Limit Line, the demarcation line between the two sides, Seoul official said, Yonhap reported. The North does not recognize the line.
North Korea, which claimed its boat was returning to port after a routine patrol, called the incident an "armed provocation" by South Korean forces in the waters of "the north side," said a statement from the Supreme Command of the Korean People's Army carried by the state media.
Xinhua, the official news agency of China which is the North's closest friend, reported Pyongyang did not say if there were any casualties on its side but that it demanded an apology from Seoul.
South Korean Rear Adm. Lee Ki-shik told reporters prior to the incident the South Koreans had fired warning shots, Yonhap reported. He said the exchange of fire lasted about two minutes and the South Korean boat took about 15 out of the about 40 shots fired by the North Koreans.
It was not clear how many shots were fired by the South but Lee said: "This is a regrettable incident in which the North directly aimed at the South. We protest sternly."
South Korean Prime Minister Chung Un-chan, while describing the incident as "accidental," told parliament the North Korean boat returned home "wrapped in flames," Yonhap reported.
The North's People's Army was quoted as saying in a statement that a "group of warships of the South Korean forces hastily took to flight."
The two Koreas remain technically in a state of war as the 1950-53 Korean War only ended in a truce.