They also touched base on the upcoming three-way summit with South Korea, set to take place next month. Japanese officials said the mutual foreign ministers' visits for the goal of bilateral talks are the first between Japan and China in eight years.
"I would like to regard [Wang's visit] as a major step forward in our efforts towards improving Japan-China relations", Kono told Wang at the start of their meeting at the Iikura Guest House.
He finally managed to turn the tide previous year with a qualified pledge of cooperation on Chinese President Xi Jinping's signature Belt and Road trade and infrastructure initiative.
Kono said that he hoped the first economic dialogue between the countries in eight years would be a "fruitful discussion".
However, he warned that there would be "no true improvement of Japan-China relations without stability in the East China Sea".
Japanese officials said Kono and Wang agreed on the importance of maintaining the world's system of free trade.
"I hope that we will be able to discuss what and China can work together on in the worldwide arena, not just bilateral issues", Kono told reporters on Friday.
But Tokyo is eager to get the relationship back on firmer footing, especially as it fears being shut out of negotiations on North Korea's nuclear programme in which Beijing is likely to be a major player.
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Now in the works is a free trade agreement between Japan, China, and South Korea, who together account for almost a fifth of global GDP.
China has demonstrated its significant influence over its reclusive ally with Xi hosting Kim and his wife in Beijing.
Wang's trip - the first of its kind in more than than eight years - comes ahead of a scheduled summit between Kim and South Korean President Moon Jae-in on April 27 in the Demilitarised Zone that divides the Koreas.
On North Korea, Kono said he and Wang "confirmed that we will work in close coordination, while fully implementing the relevant U.N. Security Council resolutions, to make the complete, irreversible and verifiable abandonment of North Korea's nuclear and missile (programs) a reality".
He will be chairing the Japan-China High-Level Economic Dialogue along with Japanese Foreign Minister Taro Kono during his three-day visit.
Mr Abe, who is due to meet Mr Trump in Florida on Tuesday to discuss North Korea, will meet Mr Wang on Monday.
The time is ripe for the two nations to improve relations to mark the 40th anniversary of their 1978 Treaty of Peace and Friendship, both ministers said.