The meeting was aimed at clarifying the fate of missing Japanese, an issue that has kept relations in a deep freeze. The talks went ahead despite concern the North's launch of missiles on Sunday, which South Korea viewed as provocative, might prompt Tokyo to pull out.
The launch "is greatly regrettable" and runs counter to the spirit of previous joint statements, said Japan's chief envoy, Junichi Ihara. His North Korean counterpart, Song Il Ho, said the launches were "fully consistent with maintaining the peace and stability in the region."
Pyongyang acknowledged in 2002 that its agents had abducted Japanese to train its spies and eventually returned five of them, along with their families. It said others Japan claimed were abducted had died or never entered the North.
Tokyo has disputed that and wants an investigation into at least 12 abduction cases. Private organisations say many more citizens were abducted. The dispute, along with concerns over North Korea's nuclear weapons, has brought relations to a virtual standstill.
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In addition to sanctions based on a set of five UN resolutions since 2006, including an arms-trade ban, a freeze of North Korean assets, a ban on people exchanges and restrictions on education and training, Japan has imposed sanctions of its own. Japan bans port calls by any North Korean-flag vessels, all trade with North Korea and the entry into Japan of North Korean citizens.
It will allow North Korean ships to make port calls for humanitarian purposes.
Japan previously agreed to lift sanctions on people exchanges and chartered flights in 2008, when North Korea agreed to open a re-investigation into the remaining Japanese abductees. But Tokyo accused Pyongyang of not abiding by that agreement and has kept the sanctions in place.
Past failures have left Japan cautious about Pyongyang's promises. Tokyo had said it wanted to study the progress and details of the investigation before announcing the end to any sanctions this time.