In November last year, the three nations declared the start of free trade talks aimed at boosting their trade, a move also seen to help ease territorial tension in the Northeast Asian region.
The three nations agreed to hold the first round of the trilateral free trade agreement (FTA) negotiations in early 2013, possibly in April or May.
"The three nations will have a two-day meeting in Tokyo from Wednesday," said an official at the ministry.
South Korea and China are currently in talks over their bilateral free trade agreement. Free trade talks between Seoul and Tokyo have been stalled since late 2004, mainly because of Japan's reluctance to lower tariffs on agricultural goods.
The ambitious three-way pact, if realized, would create one of the world's largest markets as the three nations account for 20 percent of the global gross domestic product (GDP), 17.5 percent of all global trade and 22 percent of the global population.
Data shows that the combined GDP of the three nations reached US$12.34 trillion in 2010, compared with the European Union's 30 percent and the U.S.'s 23 percent.
Trade volume among the three nations amounted to $5.32 trillion in 2010, and their combined population reached 1.52 billion.
The Northeast Asian nations' push for the free trade agreement came as the region is mired in territorial disputes and unsettled historical legacy.
Relations between Seoul and Tokyo have sunk to a record low as Tokyo renewed its claims to South Korea's easternmost islets of Dokdo after South Korean President Lee Myung-bak made an unprecedented visit to the East Sea islets in August.
Japan has experienced a similar row with China over a group of East China Sea islets.
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