The six North Korean officials met Lee at the presidential Blue House, officials said.
"I would not be surprised if the real game is to try to implant among South Korean progressives this notion that if they lean on Lee Myung-Bak to change his policy, inter-Korean relations will improve"
Paul Chamberlin, president, Korea-US consulting Inc.
"The North Koreans said they were carrying a message from [North Korea's leader] Chairman Kim Jong-Il," Yonhap quoted an unidentified government official as saying.
Paul Chamberlin, the author of Korea 2010: The Challenges of the New Millennium
, told Al Jazeera: "The North Koreans are trying to exploit rifts in South Korean politics and political society.
"Kim Dae-Jung was a progressive, he wanted to improve relations with North Korea with an engagement policy and he was succeeded by another progressive - which never really improved inter-Korea relations in any kind of substantive way.
"Now with the death of Kim Dae-Jung, they have sent their head of the spy service as the envoy for Kim Jong-il to convey a private message to Lee Myung-Bak.
"The message might be: we want to improve relations, why don't you send us humanitarian assistance. That is not likely to play out very nicely with Lee Myung-Bak's policy.
"But among South Koreans there is a desire to improve relations and I would not be surprised if the real game is to try to implant among South Korean progressives this notion that if they lean on Lee Myung-Bak to change his policy, inter-Korean relations will improve," he said.
South and North Korean officials in charge of inter-Korean relations met in Seoul for the first time in nearly two years earlier on Saturday.
Hyun told reporters that the two sides discussed various inter-Korean issues.
Kim Yang Gon, the visiting North Korean spy chief who also handles issues related to the South, said: "After meeting with several people [in the South] I felt the imperative need for North-South relations to improve."
Meanwhile, a small group of protesters staged an anti-North Korean rally close to the hotel where the North Korean delegation was staying.
Kim was cherished on both sides of the border for his pursuit of closer ties between the two states.
His "sunshine policy" engagement and aid to the impoverished North earned him the Nobel Peace Prize in 2000 and he held a landmark summit with Kim Jong-il, the North Korean leader, the same year.
The last time officials responsible for inter-Korean affairs met was in late 2007 under the administration of Roh Moo-hyun, the former South Korean president.
Cross-border tensions have risen sharply in recent months after the North made threatening gestures to the South, fired a series of missiles and staged a second nuclear test which resulted in tougher United Nations sanctions.