South Korean Defense Ministry spokesman Kim Min-seok said United States and South Korea were cooperating on missile defense but national systems would be independent.
The Yonhap news agency reports a bilateral system may spark an arms race in the region.
"South Korea has its own missile defense system for uses against missiles in the terminal stage, which is best suited for countering growing North Korean missile threats," Kim said.
Under the current circumstances, we have cooperated with the U.S. missile defense system for intelligence sharing and are seeking ways to develop the cooperation."
South Korea has Patriot missile batteries that can strike incoming missiles at an altitude as high as 18 miles.
Tensions on the Korean Peninsula have escalated since a nuclear test by North Korea in February. South Korean President Park Geun-hye told U.S. lawmakers Wednesday that North Korea's actions were undermining regional peace.
Park said Seoul was reacting to the situation "calmly" but with a sense of resolve.
"We are maintaining the highest level of readiness," she said. "We are strengthening our cooperation with the United States and other international partners."