The meeting in Tokyo was attended by the countries' chief envoys to the larger six-party talks on ending North Korea's nuclear program, the Yonhap News Agency reported.
South Korean envoy Lim Sung-nam said the meeting discussed ways of maintaining stability of the Korean Peninsula ahead of presidential elections in the United States and South Korea and constructive roles played by Russia and China in dealing with Pyongyang's nuclear ambitions.
Six party talks on North Korea's nuclear program have been dormant since 2008.
Reports of North Korean progress on its light-water reactor sparked the three-way talks.
North Korea has made "significant" progress on the project, the International Atomic Energy Agency said. The United Nations says satellite photos show a dome has been built over the facility.
South Korea is concerned the reactor is a front for stockpiling enriched uranium that can be used for bombs.