The talks held amid the international standoff over the North's pursuit of nuclear weapons, have raised hopes of a possible breakthrough in the crisis.
South Korean Unification Minister Chung Dong-young and Kim spoke and had lunch in the North's capital Pyongyang on Friday, according to pool reports.
Kim told the South Koreans he wanted to meet officials travelling with Chung whom he had previously seen, but there were no further details of their talks.
Chung was expected back in Seoul later on Friday.
He has been in North Korea since Tuesday for anniversary celebrations of a landmark summit when Kim met then-South Korean president Kim Dae-jung in June 2000.
Also attending Friday's meeting with the North Korean leader were Lim Dong-won, an intelligence chief under Kim Dae-jung's government, and then-unification minister Park Jae-kyu, pool reports said.
"It shows North Korea is making their best efforts"
South Korean prime minister
Chung's delegation had been set to return to Seoul on Friday morning but was told to remain because Kim wanted to meet them.
The reclusive Kim last met a top South Korean official in the North's capital in April 2002, before the nuclear crisis erupted later that year after US officials accused Pyongyang of running a secret uranium enrichment programme.
Kim rarely meets visiting officials, and the meeting raised hopes in the South of possible movement in the latest nuclear crisis.
"It shows North Korea is making their best efforts," South Korean Prime Minister Lee Hae-chan said in Seoul.
The North has refused to return to the nuclear disarmament talks for nearly a year, citing "hostile" US policies, and declared itself a nuclear state in February.
It has also in recent months made moves that would allow it to create more weapons-grade plutonium, adding to a stockpile experts believe is already enough to build about six nuclear bombs.