Japan's Foreign Ministry said it lodged a protest with Beijing after a Chinese maritime research ship was seen dropping a wire-like object into the water off the northwestern coast of Japanese-controlled Senkaku islands on Sunday.
China also claims the islands, which it calls Diaoyu.
The ministry said it urged China to immediately stop the survey. It said it was "extremely regrettable" that the Chinese survey ship, which did not obtain Japan's permission, was seen conducting research in the area, AP reported.
Tokyo and Beijing in 2001 agreed to give advance notice ahead of a planned maritime survey in each other's territorial waters.
The incident came amid increased Chinese activity in the area.
Also Monday, Japan's coast guard said four Chinese patrol ships violated Japanese territorial waters off the Senkaku for the second time this month.
Japan's Defense Ministry said a Chinese frigate was spotted Sunday near the Miyako Strait, and a Chinese reconnaissance aircraft was flying above the East China Sea. The latter prompted Japan to scramble a fighter jet.
Japanese warships spotted a pair of Chinese vessels — a guided missile destroyer and a fast combat supply ship — northwest of the Kume Island near Okinawa on June 10.