"The zone should not be implemented and China should refrain from taking similar, unilateral actions elsewhere in the region, and particularly over the South China Sea," Kerry told a news conference in Manila.
The Philippines warned last month that China's announcement of an Air Defence Identification Zone (ADIZ) in the East China Sea raised the prospect of it doing the same for the South China Sea.
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"Today, I raised our deep concerns about China's announcement of an East China Sea air defence identification zone," Kerry said, referring to his discussions in Manila with Philippine Foreign Secretary Albert del Rosario.
"I told the foreign secretary that the United States does not recognise that (East China Sea) zone and does not accept it."
Beijing's East China Sea air defence zone requires aircraft to provide flight plans when traversing the area, declare their nationality and maintain two-way radio communication, or face "emergency defensive measures".
The zone covers disputed Tokyo-controlled islands -- known as Senkaku in Japan and Diaoyu in China -- where ships and aircraft from the two countries already shadow each other.
Analysts warn that the ADIZ in the East China Sea is a forerunner to a similar zone in the South China Sea, which Beijing claims almost in its entirety.
Kerry, in Manila for a two-day visit, threw his support behind the Philippines over its simmering South China Sea territorial row with China, calling Manila a "key treaty ally".
Tensions between the Philippines and China have risen in recent years as Beijing becomes more forthright in asserting its claim over most of the South China Sea.
Earlier this year, Manila took Beijing to a United Nations tribunal over the contested Scarborough Shoal, which lies about 220 kilometres from the Philippines' main island of Luzon and has been controlled by Chinese government vessels since last year.
"The United States is committed to working with the Philippines to address its most pressing security challenges," Kerry said.
"That is why we are negotiating a strong and enduring framework agreement that will enhance defence cooperation under our alliance, including through an increased rotational presence in the Philippines," he said.
Both sides are in the final stages of hammering out a deal allowing more US troops, aircraft and ships to temporarily pass through the Philippines, where the last US bases closed in 1992.
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