Tokyo rejected a complaint by China's ambassador to Japan, Cheng Yonghua, according to Japan's Foreign Ministry.
Vice Foreign Minister Kenichiro Sasae told Cheng in a phone conversation that the protests in China were "regrettable" and urged Chinese authorities to ensure the safety of tens of thousands of Japanese citizens there, the ministry said.
China's official Xinhua News Agency reported protests in cities across the country. Demonstrators burned Japanese flags, overturned or smashed Japanese cars, and in some places broke windows of Japan-related businesses.
Days earlier, a group of 14 Hong Kong residents and mainland Chinese traveled by boat to the islands, some swimming ashore. Protesters in Beijing, Hong Kong and other cities praised them as heroes and burned Japanese flags, but Japan arrested the 14 for landing without authorization.
On Friday, Tokyo deported the group, seeking to quiet the regional spat. But plans for further visits by activists on both sides appear likely to further inflame the territorial tensions.
Taiwanese Foreign Minister Timothy Yang summoned Japan's de facto ambassador to Taiwan, Sumio Tarui, on Sunday to lodge a protest over the visit by the Japanese activists to the islands, which are about 190 kilometers (120 miles) off Taiwan's northeastern coast.
Yang said the "provocative act" had heightened tensions in the area, according to a ministry statement.
The spat over long-contested territories comes as China's ruling Communist Party prepares for a major leadership transition. Leaders in both China and Japan face strong domestic pressure to defend national interests.
Frictions have also flared recently over another set of disputed islands, controlled by South Korea.