Isao Iijima, a behind-the-scenes heavyweight who was also a key aide to former premier Junichiro Koizumi, flew into the isolated country, Kyodo News reported.
The agency, which has a presence in Pyongyang, said it was not known what the purpose of the visit was, but added he was greeted by Kim Chol Ho, vice director of the North Korean Foreign Ministry's Asian Affairs Department.
Footage aired on Japanese television showed the two men shaking hands on Iijima's arrival in Pyongyang.
The meeting appeared to have taken Washington by surprise, with Glyn Davies, the US State Department's special representative for North Korea, telling reporters in Seoul he had not been informed of the trip.
"I had not heard that. So that will obviously be something that I will discuss with the Japanese when I have a chance to talk to my counterparts there in a couple of days," said Davies, who is due in Tokyo later in the week.
Tokyo does not have diplomatic relations with Pyongyang and the two sides are at odds over what Japan says is the still-unresolved kidnapping of its citizens by North Korean spies in the 1970s and 80s.
Former prime minister Koizumi visited Pyongyang for talks with then North Korean leader Kim Jong Il in September 2002 and May 2004 and Iijima is known to have played a role in organising those trips.
But North Korean missile and nuclear tests in recent years have crimped relations, with Japan joining its western allies in imposing punitive sanctions on the hermit state.
Experts in Japan said recent rebukes that Beijing has doled out to its unpredictable ally over the tests, which have reportedly included the restriction of fuel imports, have left Pyongyang looking for other ways to engage the outside world.
"It could be a sign of possible resumption of dialogue as North Korea appears to have toned down its provocative approach since early May," he said, referring to threats of war Pyongyang issued last month during a joint US-South Korea military exercise.
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