The talks will be held on the sidelines of meetings by Red Cross officials from the two countries, a Japanese Red Cross spokesman said.
"The talks will be held in Shenyang on March 3," he said.
Japan's foreign ministry will sent Keiichi Ono, the head of its Northeast Asia division, to the meetings, a ministry official said.
"The Red Cross Society in North Korea approached its counterpart in Japan, requesting the meetings," the official said.
They had planned to meet again in December 2012 but that was cancelled after Pyongyang declared its plan to launch a missile.
Red Cross officials will discuss on-and-off visits by Japanese nationals to the graves of family members who died in North Korea decades ago or missions to collect their remains, the Red Cross official said.
One of the thorniest issues between Tokyo and Pyongyang is the fate of Japanese citizens who were kidnapped by North Korean agents in the 1970s and 80s.
"The meetings are scheduled to discuss the Red Cross mission," he said.
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