The two leaders also discussed China's ban on Japanese seafood and the high-profile case of a Japanese businessman detained in China during their hour-long talks on the sidelines of the APEC summit in San Francisco on Thursday evening.
The countries should "focus on common interests" and reaffirm their "strategic relationship of mutual benefit and give it new meaning", Xi told Kishida as they sat across from one another at a table flanked by their delegations.
In a joint statement in 2008, Japan and China agreed to pursue a "mutually beneficial relationship based on common strategic interests" designed to ensure frequent leadership exchanges on issues such as security.
But the phrasing has been used less frequently in recent years as the historical rivals have clashed over a series of issues such as territorial disputes, trade tensions and Taiwan, the democratic island that Beijing claims as its own.
Most recently, ties have been tested by China's ban on Japanese seafood following Tokyo's decision to release treated water from its crippled Fukushima nuclear plant into the sea in August.
In comments to the media after the talks, Kishida said he had strongly urged Xi to drop the ban and also sought the swift release of the businessman, which has dealt an outsized blow to their close economic ties.
Xi said Japan should take concerns about the water release from Fukushima seriously and handle the discharge responsibly, China's official Xinhua news agency said.
The two sides also pledged to hold high-level dialogues on economic issues and welcomed the launch of a new framework to discuss export controls, Japan's foreign ministry said.
Alongside the United States, China is Japan's top trading partner.
The Kishida-Xi meeting followed a summit between US President Joe Biden and Xi in which the two superpowers agreed to open a presidential hotline and resume military-to-military communications.
Kishida also met Biden at the summit where they discussed issues including "common challenges" that they share with China.
