Rodong Sinmun, the official newspaper of the ruling North Korean Workers' Party, published a commentary saying: "If this group of traitors keeps to the route of reckless confrontation with the DPRK [North Korea], defaming its dignity despite repeated warnings, this will compel it to make a crucial decision including the total freeze of North-South relations."
The comments were quickly played down by South Korea's Unification Ministry, which said they did not represent Pyongyang's official position.
South Korean analysts have interpreted the North Korean threat as an attempt to create a rift between Seoul and Washington.
South Korea's President Lee, who took office in February, has strengthened ties with the U.S., while warning that further economic aid to the North could be withheld if Pyongyang fails to meet its nuclear disarmament commitments. He has also pledged to review agreements on bilateral economic projects agreed at North-South summits.
His stance has come as a sharp contrast to that of his two predecessors, who agreed to massive subsidies for the impoverished North in a drive to rebuild relations.
The North Korean commentary accused Lee of "trampling" on the summit agreements in pursuit of confrontation with the Pyongyang.
The article came days after the United States removed the North from its terrorism blacklist. In response, Pyongyang said it would restart work to disable its nuclear facilities.