Junichi Ihara, who heads the Japanese foreign ministry's Asian and Oceanian affairs bureau, made the protest by phone to Han Zhiqiang, minister at the Chinese Embassy in Japan, the ministry said in a statement.
He said Japan could "never accept the zone set up by China" as it includes the Tokyo-controlled Senkaku islands, the statement said.
China also claims the islands, calling them Diaoyu.
Ihara also told the Chinese side that such move by Beijing would "escalate" current bilateral tensions over the islands, branding it "very dangerous".
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Along with the creation of the zone in the East China Sea, the Chinese defence ministry released a set of aircraft identification rules that must be followed by all planes entering the area, under penalty of intervention by the military.
Aircraft are expected to provide their flight plan, clearly mark their nationality, and maintain two-way radio communication allowing them to "respond in a timely and accurate manner to the identification inquiries" from Chinese authorities.