The three men will meet in Seoul on Saturday, a Japanese foreign ministry official said.
"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.
He added no date had been set yet for a three-way leaders' summit, which was last held in May 2012.
The upcoming Seoul meeting will be the first among foreign ministers of the three countries since April 2012.
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South Korean President Park Geun-Hye has held two summits with Chinese President Xi Jinping, but only sat down with Japanese Prime Minister Shinzo Abe at the 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.
As well as a dispute over some South Korea-controlled islets, Seoul feels Tokyo has yet to fully atone for the excesses of its colonial rule and the forced recruitment of South Korean women to wartime military brothels.
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.
Relations soured further in 2012 when the Japanese government angered China by nationalising some of the islands.
Since then, Tokyo and Beijing have routinely clashed over the issue, with official Chinese ships and aircraft regularly testing Japanese forces.