Six-party negotiations on North Korea's nuclear program stalled after Pyongyang failed last December to disclose full information on its nuclear work.
Japan's Yasuo Fukuda told reporters after the meeting with Lee Myung-bak: "Our three countries will do everything possible to ensure that the Korean peninsula becomes nuclear-free."
"We agreed that South Korea and Japan would work together and that Japan, South Korea and the United States would cooperate more closely than previously," he said.
Pyongyang started disabling its Yongbyon nuclear plant late last year as part of a deal with the U.S., China, Russia, Japan and South Korea in exchange for economic aid and diplomatic incentives. North Korea tested a nuclear bomb in October 2006.
A U.S. delegation is expected to visit Pyongyang for further denuclearization talks on Tuesday.
Lee has taken a tougher stance on North Korea than his predecessor, Roh Moo-hyun, bringing the South Korean position closer to that of Tokyo. He has repeatedly said he plans to seek more in return from Pyongyang for South Korea's generous subsidies, and last month urged North Korea to cooperate on the issue of repatriating abductees and prisoners of war.
Relations between Japan and South Korea soured after Seoul suspended annual summits in 2005 over then-Prime Minister Junichiro Koizumi's repeated visits to a Tokyo war shrine seen as a symbol of Japanese militarism, and Japan's reluctance to apologize for the 1910-1945 occupation of Korea.
However, since Lee's election as president last December, the new leader has taken steps to mend ties with Japan. At today's talks, the leaders agreed to resume summit diplomacy and regular consultations on an economic partnership agreement, and the South Korean leader announced plans for an industrial park in South Korea for Japanese producers.
