The North and South have been formally at war since 1950, never having signed a formal peace agreement ending the conflict.
Speaking to reporters in Seoul Lee said he intends to absorb the Unification Ministry into the foreign ministry, but added that "utmost efforts" would be made to promote dialogue and exchanges with the North.
"We will continue to persuade North Korea that giving up its nuclear weapons programmes will benefit both the regime and its people," he said.
Last week Lee said he was willing to hold a summit meeting with North Korea's leader Kim jong-il, although he hoped such a meeting would be held in the South Korean capital.
The only two prior summits between the leaders of North and South Korea were both held in Pyongyang.
Lee is due to be sworn into office on February 25.