Saturday's meeting is the first between officials from the two Koreas since the conservative Mr Lee came to power in Seoul in February 2008.
Relations soured when Mr Lee made South Korean aid conditional on North Korea's nuclear disarmament.
In the past few months, North Korea has fired a long range rocket over Japanese territory and conducted an underground nuclear test.
But more recently, there has been a series of conciliatory gestures. Two US reporters and a South Korean worker were released from detention and Pyongyang said it was interested in resuming cross-border tourism and industrial projects.
Some observers believe that, with UN sanctions beginning to bite, the North is keen to boost cross-border tourism and trade that bring in badly needed foreign currency, our correspondent adds.
On Friday, the six officials from North Korea's ruling Workers' Party, wearing black suits and ties, placed a wreath of flowers on the steps of South Korea's National Assembly, where Kim Dae-jung is lying in state.
Mr Kim - who died on Tuesday at the age of 85 - devoted his presidency to improving relations between the two Koreas, still technically at war.
He reached out to the North with aid - the main thrust of his "Sunshine Policy" that earned him the Nobel Peace Prize in 2000, and held a historic summit with Kim Jong-Il in that year.
Mr Kim's funeral is to be held on Sunday.