The reversal comes after pressure from the Japanese government, which insisted China's announcement was invalid, and after governments around the world lined up alongside Tokyo.
Japan's two major airlines had previously said they had been submitting flight plans to Chinese authorities for any plane that was due to pass through the area, a key demand Beijing set out on Saturday when it said it had established an Air Defence Identification Zone (ADIZ).
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The move heightened tensions in the region, where temperatures were already running high over the ownership of the Tokyo-controlled Senkaku islands, which Beijing says it owns and calls the Diaoyus.
Yesterday it was roundly condemned by Japan and its allies, including the United States, which flew two US B-52 bombers over the disputed islands in a show of force.
"After the Japanese government said private airlines don't have to follow Beijing's claims on Tuesday, our industry body held a meeting on Tuesday and decided we won't follow" Beijing's demands any more, a spokesman for former flag carrier Japan Airlines told AFP.
"JAL has stopped submitting flight plans since 0000 am today (1500 GMT yesterday)," he said.
JAL's rival All Nippon Airways also said it has stopped complying.
"The Scheduled Airlines Association of Japan, an aviation industry body, made the decision after it received assurances from China, through the Japanese foreign ministry, that Beijing has no intention of obstructing the flights of commercial airline carriers," the JAL spokesman said.