The paper said the clash was not accidental but stemmed from a plan "to turn inter-Korean relations toward tension through the means of military provocation".
According to South Korea's joint chiefs of staff, the clash occurred when a North Korean patrol boat crossed the disputed border line in the Yellow Sea before noon on Tuesday, drawing warning shots from a South Korean navy vessel.
The North Korean boat then opened fire and the South's ship shot back, apparently badly damaging the North Korean ship which then sailed back toward its waters.
The Koreas blame each other for causing the skirmish in the rich crab-fishing area, where both sides regularly accuse the other of border violations.
The North Korean military claims its ship was attacked by South Korean vessels as it was returning from checking on "an unidentified object that intruded" into its waters.
As the accusations continue, South Korea on Wednesday ordered two more warships to the area to guard its border.
Military sources told the AFP news agency that the patrol boats would "reinforce vigilance" along the Yellow Sea border.
Kim Tae-young, the defence minister ordered army, navy and air force commanders along the border with the North to increase surveillance and respond immediately to any provocation.
However a spokeswoman for the South Korean president said the government wanted to ensure the clash did not damage cross-border relations.