Japanese Prime Minister Shinzo Abe is the only leader from a major stakeholder country to not publicly arrange a meeting with North Korea's Kim Jong Un this year.
During the meeting, which marked the resumption of the trilateral leaders' meeting mechanism after a two-and-a-half-year hiatus, the three sides agreed to meet on a regular basis to expand their common interests and manage disputes.
After tripartite talks between China, Japan and South Korea on regional free trade deals and the China-led Regional Comprehensive Economic Partnership, Chinese Premier Li Keqiang batted for "new progress" between Beijing and Tokyo.
Abe, for his part, pledged Tokyo's adherence to free trade.
The Chinese premier also suggested that China, Japan and South Korea join hands to promote the building of an East Asian Economic Community, and stand together in an even more steadfast manner to safeguard the rules-based multilateral free trade system. "Through actual behaviour, let's show that we three nations support engaging in free trade".
Japan and South Korea have been involved in a prolonged row over the disputed islands known as Dokdo in South Korea and Takeshima in Japan.
Li announced the decision during his meeting with Japanese Prime Minister Shinzo Abe in Tokyo.
During the meeting, Li also pointed to energy efficiency, environmental protection, scientific and technological innovation, high-end manufacturing, finance, sharing economy, and gerontics services as key areas where China and Japan should enhance cooperation.
On Thursday Li attended an event marking the 40th anniversary of the China-Japan peace treaty in Tokyo.
China, Japan and South Korea began free trade agreement talks in November 2012, with the latest round of talks being held in Tokyo.
"We very much look forward to a more open and inclusive business environment, in which companies can "go global". with reassurance among the three countries as a result of improved exchanges and collaboration made possible by this summit", Yuan said.
On Wednesday, China, Japan and South Korea agreed to cooperate in seeking the denuclearization of the Korean Peninsula.