Japanese Foreign Minister Fumio Kishida told reporters in Tokyo that the government-level talks will be held on May 26-28 in Stockholm.
It will come after the two countries held their first official talks in 16 months in March, speaking on a range of issues, including the abduction issue and North Korea's nuclear weapons programme.
While relations with South Korea continue to be testy, Pyongyang's approach to its dealings with Japan appears to have softened in recent months, especially on the emotive issue of abductions.
Five of the abductees were allowed to return to Japan, but Pyongyang has insisted, without producing solid evidence, that the eight others are dead.
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"Needless to say, the abduction issue is one of the nation's biggest concerns," Kishida said. "We would like to draw their positive response."
During the March meeting, the Japanese side also protested against the communist state's launch of ballistic missiles and its threat to conduct more nuclear tests.
Formal ties with Japan could bring huge economic benefits to the impoverished state.