The meeting in the Swedish capital takes place after the two countries held their first official talks in 16 months in China in March, addressing a range of subjects including the abduction issue and North Korea's nuclear weapons programme.
Prior to the discussions at a small Stockholm hotel, the two delegations -- eight on either side -- appeared briefly in front of the media, the majority Japanese reporters flown in for the occasion.
"Over the next three days, we want to hold forward-looking talks, based on issues we raised at the government talks in Beijing," said Japanese chief delegate Junichi Ihara, the director general of the foreign ministry's Asian and Oceanian Affairs Bureau.
"We also want to make an effort to push for a resolution of various issues as much as possible by frankly and seriously discussing broad matters of mutual interest."
His North Korean counterpart Song Il Ho, wearing a bright red and gold badge with the image of Kim Jong-Un and his grandfather Kim Il-Sung, said that "we hope to hold sincere, deep and wide-ranged talks on relations between North Korea and Japan."
North Korea's approach to its dealings with Japan appears to have softened in recent months, especially on the emotive issue of abductions.
North Korea outraged Japan when it admitted more than a decade ago that it had kidnapped 13 Japanese in the 1970s and 1980s to train its spies in Japanese language and customs.
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