Foreign minister Fumio Kishida called in Cheng Yonghua, Beijing's envoy to Tokyo, the foreign ministry said -- the second such summons since Friday.
"The situation surrounding the Japan-China relationship is markedly deteriorating," he told Cheng, according to the ministry's statement on its website.
"We cannot accept that (China) is taking actions that unilaterally raise tensions."
The two countries are locked in a long-running dispute over the uninhabited islets known as the Senkaku in Japan and the Diaoyu in China.
Cheng was also summoned on Friday by vice minister Shinsuke Sugiyama after two Chinese coast guard and fishing vessels entered Japan's territorial waters.
On Tuesday morning, the Japan Coast Guard said it spotted Chinese ships in the country's territorial waters surrounding the islands and about a dozen others nearby.
The Japanese coastguard a day before caught sight of 15 Chinese coast guard ships near the islands -- the highest number ever spotted.
It is rare for so many Chinese fishing vessels to be seen in the disputed waters.
Tensions over the islands have been a frequent irritant and have strained bilateral relations, though tensions had markedly relaxed over the past two years as two sides took steps to ease the pressure through dialogue.
But the fundamental divide over the islands remains unresolved.
Japan's Kyodo News reported Monday that Japan wants "high-level" talks with China over the incursions as they have not stopped despite Tokyo's protests.
Japan protested in June after it said a Chinese navy frigate sailed close to territorial waters near the islands for the first time.
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