Shinzo Abe said Tokyo judged Pyongyang, which has pledged to re-investigate the disappearances of Japanese citizens, had shown sufficient willing in resolving the decades-old row and that this needed to be reciprocated.
"We have concluded that an unprecedented scheme that can make national decisions has been established. In accordance with the principle of action to action, we will lift part of the measures taken by Japan," Abe told reporters.
The move comes after the two sides met in Beijing to discuss what happened to the dozens -- or even hundreds -- of people Japan says were snatched by North Korean spies to train their agents in language and customs during the 1970s and 1980s.
"North Korea appears to be showing its seriousness, and the Japanese response is reasonable," said Satoru Miyamoto, a North Korea expert at Seigakuin University in Saitama, north of Tokyo.
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"But this is just the beginning as no one knows about what the results will be," Miyamoto said.
"Prime Minister Abe has taken a gamble and will have to make tough, political decisions from now on," he said.
Japan and North Korea do not have formal diplomatic ties and relations between the two have been testy for decades.
Abe's announcement coincided with a visit to South Korea by Chinese President Xi Jinping, which is largely seen as snub to the North, Beijing's traditional ally.
Kim Geun-Shik, professor of politics at South Korea's Kyungnam University, said the diplomatic chill rippling through northeast Asia, in which Tokyo remains at odds with both Beijing and Seoul, was a factor.
"Japan, like the North, is faced with increasing diplomatic isolation in the region with its relations with the South and China showing no signs of improvement under Abe's hawkish administration," he said.
The South Korean foreign ministry today said it recognised the "humanitarian" nature of the issue but warned Japan against undermining efforts to force North Korea to abandon its nuclear weapons.
"Any measures taken by the Japanese government should not hurt international coordination among South Korea, the United States and Japan over North Korea's nuclear and missile programmes," the ministry said.
South Korean officials say Pyongyang is using the kidnapping issue to exploit that fragile alliance and push Tokyo towards a more independent North Korea strategy.