Japan lodged a protest with China after one of its naval survey vessels entered Japanese waters on Saturday, the second incursion into its territory by the Chinese military in less than a week.
An uptick in Chinese military activity near Japan and around Taiwan in recent years has stoked concerns in Tokyo. Japan has responded with a defence buildup that it says aims to deter Beijing from using military force to push its territorial claims in the region.
The ship was detected off the coast of Kagoshima Prefecture, in Japan's southwest, at around 6 a.m. local time (2100 GMT Friday), and departed within two hours, the country's defence ministry said.
Tokyo registered its "strong concern and protest over this incident" with a Chinese embassy official, the foreign ministry said in a statement that also referenced the first airspace intrusion by a Chinese military plane on Monday.
Tokyo told Chinese diplomats earlier this week that Monday's violation of it airspace was "utterly unacceptable."
A telephone call to the Chinese embassy in Tokyo went unanswered when Reuters called outside regular business hours.
Saturday's incident was the tenth time in the past year that a Chinese naval survey ship has sailed through Japan's territorial waters, and the 13th time if submarines and other intelligence-gathering vessels are included, according to national broadcaster NHK.