Abe also invited Chinese President Xi Jinping to visit Japan next year.
U.S. President Donald Trump, who had previously backed Abe's push for maximum pressure on Pyongyang, is now scheduled to meet with Kim before mid-June.
The meeting comes amid a flurry of developments on the Korean Peninsula.
The US has been hesitant to make any specific pledges to North Korea on what would happen in return for denuclearization.
In response, the Emperor said he "hopes that Japan and China will further boost their relations of friendship and goodwill", according to the Imperial Household Agency.
Chinese Premier Li Keqiang also attended the three-way summit, which was last held in Seoul in 2015.
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In talks with Moon later on Wednesday, Abe expressed Japan's concern that pressure on North Korea might be lifted too early as a "reward" for its shutting down its nuclear test site or halting missile launches.
"We are all beneficiaries of free trade and even though various issues have emerged, these should not stand in the way", Li said.
On Wednesday, both South Korean President Moon Jae-in and Chinese Premier Li Keqiang noted that North Korea should be guaranteed economic aid by the global community once it undertakes complete denuclearization.
Commenting on Wednesday's meeting between Chinese Prime Minister Li Keqiang, South Korean President Moon Jae-in and Japanese Prime Minister Shinzo Abe, Li Kai of Shanxi Finance University told Sputnik about a proposed free trade zone between the three countries. Li also talked of intentions to set up a yuan-clearing house in Tokyo.
China had also resisted Japan's insistence that the agreement should not cover the territorial waters surrounding the islets, controlled by Japan. The pact provides for meetings between both nations' defence officials and a mechanism for their naval vessels to communicate at sea to avert maritime incidents. "If Japan does not take advantage of this opportunity, discussions on North Korean issues will likely proceed at the exclusion of Japan".