The meeting in Seoul is likely to focus on ways to ease regional tensions over territorial and diplomatic disputes.
The three states have strong economic ties but relations still suffer from unresolved issues dating back to Japan’s actions in World War Two.
A Chinese foreign ministry spokesman said he hoped the ministers would be able to “look forward into the future”.
South Korea’s Yun Byung-se welcomed Japan’s Fumio Kishida and China’s Wang Yi to South Korea’s capital on March 21.
Foreign ministers from China, Japan and South Korea last met in April 2012, for their sixth annual trilateral meeting.
It was cancelled the following year after Japanese PM Shinzo Abe angered China and South Korea by visiting a shrine that honors Japan’s war dead, including a number of senior war criminals.
China and South Korea have accused Tokyo of failing to adequately atone for aggression in World War Two, including its wartime use of s** slaves, known euphemistically as “comfort women”.
They also accuse Japan of whitewashing wartime atrocities in schoolbooks.
Chinese Foreign Minister Wang Yi expressed hope that South Korea would join the China-led Asian Infrastructure Investment Bank (AIIB) and South Korea’s Yun Byung-se said Seoul was reviewing its options, a South Korean official told Reuters after the meeting of the two ministers.
Fumio Kishida met his South Korean counterpart ahead of the trilateral meeting, and said that “despite difficult issues between the two countries”, the two sides would “continue communicating at various levels in order to strengthen our co-operation”.
The resumption of the foreign ministers’ meeting has fuelled hopes that a summit of the counties’ three leaders could be held later this year.
The poor relationship between Japan and South Korea has become a concern for the US, which sees the two countries as its main military allies in Asia.
Last week, US Assistant Secretary of State Daniel Russel described the tension between its “two friends” as a “strategic liability”.
Saturday’s meeting comes just days after China and Japan held their first high-level security talks in four years.
Those discussions are believed to have centered on the creation of a maritime communication hotline between the countries, following tensions over islands in the East China Sea.
There have been several disputes in recent years over the islands, known as Senkaku in Japan and Diaoyu in China, and officials have expressed fears that a clash could trigger a full-blown conflict.
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