The North's offer for "unconditional and early" talks comes as the U.S. envoy on the North was in the region to discuss the standoff.
Tensions between the Koreas have been at their highest level in years since the North showered artillery on a South Korean border island of Yeonpyeong in November. Four South Koreans were killed in the attack.
The attack was the first on a civilian area since the 1950-53 Korean War, and occurred in waters not far from the spot where a torpedo sank a South Korean warship eight months early, killing 46 sailors.
The marine attack was also blamed on the North, an allegation the country strongly denies.
However, on New Year's Day, the North Korean government issued a statement calling for warming ties and future joint projects with South Korea.
Monday, South Korean President Lee Myung-bak vowed to increase defenses but also said the door was open for talks with the North. He also said he was willing to enhance economic cooperation between the two rivals.
On Wednesday, North Korean officials responded with their own call for negotiations.
"We are ready to meet anyone anytime and anywhere, letting bygones be bygones, if he or she is willing to go hands in hands with us," said a statement carried by the North's official Korean Central News Agency. It added that history has shown that such confrontations can only lead to an "armed clash and war."
South Korea's Unification Ministry immediately rebuffed the overtures late Wednesday.
"We don't consider it as a sincere offer of dialogue," ministry spokeswoman Lee Jong-joo said. North Korea first must apologize for the two attacks and take "sincere" steps toward nuclear disarmament, she said.
North Korea will be a key issue during Chinese President Hu Jintao's visit to Washington later this month.
The Associated Press contributed to this report.