Deputy Foreign Minister Song Min-Soon said in an interview with Yonhap news agency that the missile was not capable of carrying a nuclear warhead.
"The missile that North Korea recently launched is a short-range missile with a range of some 100 kilometers (62 miles) and is far from the one that can carry a nuclear weapon," Song told Yonhap.
"This is not a case to be linked to the nuclear dispute."
Japanese media first broke the news about the North's test-firing of a missile on Sunday with broadcaster NHK saying it flew 100 kilometers from North Korea into the Sea of Japan (East Sea).
The launch came as North Korea was locked in a standoff with the United States and its allies, including Japan, over its nuclear ambitions.
Six-way talks, which include the two Koreas, Russia, Japan, the United States and China, have been stalled for nearly a year since a third round of negotiations in June last year.
The North has boycotted the nuclear disarmament talks since it failed to show up at a fourth round scheduled for Beijing last September, citing "hostile" US policy towards the communist state.