The three-day talks, marking the first round of the FTA effort, will discuss the scope of the negotiations, the South Korean government said.
The countries decided in November to proceed with talks to boost trade. South Korea's Yonhap news agency said the talks are seen as a way to deal with territorial issues.
South Korea and China are already involved in talks for a bilateral free trade agreement. Similar talks between South Korea and Japan haven't proceeded since 2004 because of Japan's reluctance to lower tariffs on agricultural goods, the report said.
A FTA among the three countries would create one of the world's largest markets as they together account for 20 percent of the global gross domestic product and 17.5 percent of all global trade, Yonhap reported. The combined GDP of the countries totaled $12.34 trillion in 2010.
Japan's territorial dispute with China over the Senkaku Islands in the East China Sea has worsened since Japan nationalized the islands in September. The islands are also claimed by China and the dispute has affected bilateral trade.
Relations between Japan and South Korea also have been affected over the South Korean-controlled island called Takeshima by Tokyo and Dokdo by Seoul.