Five officials, including Japan's deputy foreign minister Hitoshi Tanaka and Mitoji Yabunaka, head of the ministry's Asian and Oceanian affairs bureau, were expected to arrive in Pyongyang around 6:00pm (0900 GMT), he said.
"They will be meeting with foreign ministry officials of the North Korean government and they will discuss the bilateral issues including abductions and also at the same time nuclear issues," spokesman Hatsuhisa Takashima said.
The delegation will stay in Pyongyang until Saturday, he said. "We have been urging North Koreans to reopen bilateral talks... and recently they responded to us positively through the embassy route in Beijing," Takashima said.
The Japanese delegation will press for the return of relatives living in North Korea of five Japanese abducted by North Korean spies in the 1970s and 1980s.
"That is priority number one as far as we are concerned,"
Five surviving kidnap victims were allowed to return to Japan in October 2002, but there are growing Japanese calls for their families left behind in North Korea to be allowed to leave too.
"We have been urging North Koreans to reopen bilateral talks... and recently they responded to us positively through the embassy in Beijing"
Japanese foreign ministry spokesman
Japan believes more abductees are still alive and that dozens more Japanese might have been kidnapped.
Takashima said it was unclear what conditions North Korea might demand for the relatives' return.
Meanwhile, the United States on Wednesday said China recognised North Korea had become a "serious strategic problem" and urged it to show solidarity in calls for Pyongyang to dismantle its entire nuclear programme.
Washington argues that upcoming six-party talks in Beijing must focus on North Korea's covert uranium-based programme, as well as on its well-documented plutonium-producing enterprise.
North Korea says the uranium programme does not exist and China too continues to view with scepticism the US allegations on uranium.
KCNA, North Korea's official news agency, said on Tuesday it had received support from Beijing for its proposal to freeze its programme in return for economic concessions from the United States, rather than a complete dismantling.