The uninhabited outcroppings in the East China Sea, called Senkaku in Japanese and Diaoyu in Chinese, are controlled by Japan but also claimed by China and Taiwan.
Tensions over the tiny islands intensified after Tokyo bought them from their Japanese private owners in September, prompting Chinese to hold demonstrations and boycott Japanese products.
The latest incident was the 21st and longest intrusion by Chinese vessels into what Japan considers its territorial waters around the islands since that purchase, the coast guard said.
Deputy Foreign Minister Akitaka Saiki summoned Ambassador Cheng Yonghua to the Ministry of Foreign Affairs after the four Chinese government ships entered waters off the islands for about 13 hours Monday until early Tuesday, ministry official Masaru Sato said.
Asked about the reprimand during a routine briefing, Chinese Foreign Ministry spokesman Hong Lei reiterated Beijing's stance that the islands are "an inherent part of Chinese territory," and said the Chinese vessels were carrying out normal official duties.
"We do not accept Japan's protests and representations," Hong said.
"Despite China's objections, Japan sent vessels and planes to the waters and airspace of the Diaoyu Islands for many times. China made representations many times, urging Japan to stop illegal acts that violated China's sovereignty," he said.
On Dec. 13, a Chinese government airplane flew into airspace above the islands, prompting Tokyo to launch a formal protest. Beijing said the plane was conducting a normal operation.