All Nippon Airways (ANA) said that since Sunday it has been submitting flight plans to Chinese authorities for any plane that was due to pass through the area. Its affiliate Peach Aviation said it was doing the same "for now".
The announcements came after former flag carrier Japan Airlines said it was complying with demands Beijing set out on Saturday when it said it had established an Air Defence Identification Zone (ADIZ) where all aircraft were required to obey its orders.
"We have taken the measures in line with international regulations," an ANA spokesman said. "Safety is our top priority. We have to avoid any possibility of the worst-case scenario."
Peach Aviation said it had taken similar steps. "We will continue submitting our flight plans to the Chinese side for now," a spokesman said.
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Transport Minister Akihiro Ota insisted that the Chinese declaration was "not valid at all" and called on Japanese airlines to ignore it.
Under the rules 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 identification inquiries from Chinese authorities.
The area also includes waters claimed by Taiwan and South Korea, which have also both registered their displeasure at the move.