The three men will meet in Seoul on Saturday, a Japanese foreign ministry official said, the first time the countries' top diplomats have held talks since April 2012.
"Cooperation among the three countries is important for Japan and we naturally hope this foreign ministers' meeting will lead to a summit in the future," the official said.
No date had been set yet for a three-way summit, he added. Leaders from the three countries last met in May 2012.
"Foreign ministers of the three countries will review the progress made during trilateral cooperation and exchange views on the principles that should be held and the future direction of trilateral cooperation," he told reporters in Beijing.
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While relations between China and South Korea are strong, both have strained ties with Japan, chiefly because of historical and territorial disputes.
Japan and China have long been at odds over the sovereignty of uninhabited islands in the East China Sea, which Japan administers and calls the Senkakus, but which China claims as the Diaoyus.
Since then, Tokyo and Beijing have routinely clashed over the issue, with official Chinese ships and aircraft regularly testing Japanese forces.
Japanese Prime Minister Shinzo Abe and Chinese President Xi Jinping staged a frosty handshake on the sidelines of the Asia-Pacific Economic Cooperation forum in November, but ties remain under pressure.
South Korean President Park Geun-Hye has held two summits with Xi, but only sat down with Abe at a three-way summit under pressure from Washington.
Seoul-Tokyo ties have always been problematic, given the bitter legacy of Japan's 1910-45 rule over the Korean peninsula.
The friction is a source of irritation for Washington, which would rather its two key regional allies could bury the hatchet and instead focus on forming a united front against an increasingly assertive China.