Akitaka Saiki said the North Korean delegation to the talks in Beijing agreed to set up the three working groups to discuss Japanese abducted to North Korea in the 1970s and 1980s, North Korea's nuclear weapons and ballistic missile programs and Pyongyang's demand for compensation for Japan's 1910-1945 colonial rule over the Korean Peninsula.
"The North Koreans have agreed to have separate talks on these issues," Saiki told reporters.
Japan had proposed establishing the working groups at Japanese-North Korean talks in November. Saiki said the next round of negotiations would take place in Beijing in late January.
Setting out for the second and last day of this session of negotiations early Sunday, Saiki emphasized the importance of setting up the working groups.
"The most important issue to be discussed today is the principle that needs to be established between the two countries," he said. "Only when we agree on starting talks on ... major issues, can we start sharing the ideas of principles."
The Pyongyang Declaration of 2002 committed the sides to working to normalize diplomatic relations. However, Japan has indicated that progress is contingent on North Korea providing a full accounting of Japanese abducted to train North Korean spies in Japanese language and culture.
North Korea in 2002 acknowledged abducting 13 Japanese citizens and allowed five of them to return to Japan. It said the other eight died, but many in Japan suspect some might still be alive.
"The most important issue is the abductions," Chief Cabinet Secretary Shinzo Abe told reporters in Tokyo on Saturday. "We expect a sincere response from North Korea."
Impoverished North Korea is eager to establish relations with Japan in hopes of winning investment and development aid, while Tokyo is primarily interested in neutralizing the military threat from Pyongyang.
Japan and North Korea met for two days last month for the first time in more than a year. But the talks ended in discord over the North's demands for compensation and Japan's demands over the abductions.