Japan's foreign ministry on Friday summoned China's ambassador to protest what it said were intrusions into its territorial waters by Chinese coast guard and fishing vessels.
The two countries are locked in a long-running dispute over uninhabited islets in the East China Sea known as the Senkaku in Japan and the Diaoyu in China.
Japanese vice foreign minister Shinsuke Sugiyama called in Cheng Yonghua, Beijing's ambassador to Tokyo, the foreign ministry said in a statement on its website.
Sugiyama "strongly protested" to Cheng that the incursions were a "violation of Japan's sovereignty", the ministry said.
Japan also issued separate protests to other officials at the Chinese embassy in Tokyo as well as through its own embassy in Beijing to China's foreign ministry, the statement said.
The Japan Coast Guard, meanwhile, said in a statement that two coast guard vessels from China's State Oceanic Administration entered territorial waters near the Senkaku islands during the afternoon before eventually departing.
One ship entered Japan's waters twice, it said, while a Chinese fishing boat was also seen in violation.
Japan's coast guard said that it warned all the vessels to leave.
Tensions over the islands reached their peak in late 2012, seriously harming bilateral relations.
The two sides have gradually taken steps to ease tensions through dialogue but the fundamental divide over the islands remains unresolved and tensions occasionally flare up.
Japan also lodged a protest in June after it said a Chinese navy frigate sailed close to territorial waters near the islands for the first time.
Japan said in an official annual defence report on Tuesday that China has been stepping up activities in the area, including flying aircraft closer to the islets.
China is also embroiled in an increasingly bitter dispute over territory in the South China Sea with several Southeast Asian countries.