"It is extremely regrettable that China is proceeding with unilateral development in the area while the boundary between Japan and China in the East China Sea is not yet fixed, despite [our] repeated protests," government spokesman Yoshihide Suga told reporters on Wednesday.
However, the protest has been ignored by the Chinese side.
"They are totally within the scope of China's sovereign rights and jurisdiction," Foreign Ministry spokesman Geng Shuang told a regular news briefing.
Japan and China have long disputed the boundaries of their exclusive economic zones in the East China Sea. China does not recognize the proposed median line and says its EEZ stretches further to the edge of the continental shelf, closer to Japan's Okinawa Prefecture.
They are also at odds over the Senkaku Islands in Japan and the Diaoyu Islands in China.