But the pair agreed to work to expand cultural exchanges and continue high-level dialogue on the economy, both Tokyo and Beijing said after the talks on the sidelines of the Asia-Pacific Economic Cooperation (APEC) summit in Peru.
The meeting comes after Ishiba kept his job as prime minister in a parliamentary vote this week despite having led the ruling coalition to its worst election result in 15 years.
Relations between Japan and China have worsened as Beijing builds up its military capacity in the region and Tokyo boosts security ties with the United States and its allies.
Ishiba "conveyed serious concerns over the Chinese military's growing activity" to Xi, the Japanese foreign ministry said.
He stressed that "the peace and stability of the Taiwan Strait is extremely important to Japan and the international community, while also expressing serious concerns over the situation surrounding the South China Sea, Hong Kong and Xinjiang".
China has ramped up military pressure on self-ruled Taiwan in recent years to pressure Taipei into accepting its claims of sovereignty, which the island's government rejects.
Beijing has also in recent months pressed its sweeping territorial claims in the East and South China Seas more stridently.
A chain of uninhabited islands claimed by Beijing but administered by Tokyo, known as the Senkaku in Japan and Diaoyu in China, have long been a point of tension between the neighbours.
Xi said he hoped Japan would work with China to "properly handle major issues of principle such as history and Taiwan" and "manage differences constructively," according to a statement from the Chinese Ministry of Foreign Affairs.
China and Japan, "whose economic interests and industrial and supply chains are deeply intertwined," need to "pursue win-win cooperation and maintain the global free trade system as well as stable and unimpeded production and supply chains", Xi said.
Tokyo said they had agreed to "work towards realising mutual visits by respective foreign ministers, as well as the high-level dialogue on cultural exchange and economy".
Another recent flashpoint in bilateral ties was the fatal stabbing in September of a 10-year-old Japanese schoolboy in Shenzhen.
Ishiba urged Xi to "strengthen measures to ensure the safety of Japanese citizens" living in China, while Xi promised that the "safety of foreign nationals including Japanese people will be secured," Japan's foreign ministry said.
At APEC, Ishiba also met outgoing US President Joe Biden and held trilateral talks with Biden and South Korean President Yoon Suk Yeol.
"We strongly oppose any unilateral attempts to change the status quo" in Asia-Pacific waters, the three leaders said in a joint statement, without mentioning China directly.
"We steadfastly oppose the dangerous use of coast guard and maritime militia vessels and coercive activities in the South China Sea," it said.
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