Japan’s aircraft had conducted routine “surveillance activity” over the East China Sea zone, the top government spokesman said.
South Korea had also conducted a flight, its defense ministry said.
China says planes transiting the zone, which covers areas claimed by Tokyo, Seoul and Taipei, must file plans.
The zone includes islands known as Senkaku in Japan and Diaoyu in China which are claimed by Japan, China and Taiwan.
Japan controls the islands, which have been the focus of a bitter and long-running dispute between Japan and China.
The zone also covers a submerged rock that South Korea says forms part of its territory.
China, which established the air defense identification zone (ADIZ) on Saturday, says aircraft must report a flight plan, communicate and identify themselves. Those who do not could face “defensive emergency measures”.
China’s move has been condemned by the US and Japan.
The US, which called the move a “destabilizing attempt to alter the status quo in the region”, flew two unarmed B-52 bombers through the zone unannounced on Tuesday.
Japanese officials did not specify when the flights happened, but confirmed the surveillance activity.
“Even since China has created this airspace defense zone, we have continued our surveillance activities as before in the East China Sea, including in the zone,” said Japan’s top government spokesman, Yoshihide Suga.
“We are not going to change this [activity] out of consideration to China,” he added.
For their part, South Korea’s military said one of their planes entered the zone on Tuesday.
South Korea’s Foreign Minister Yun Byung-se said on Wednesday that the air zone issue had made “already tricky regional situations even more difficult to deal with”.
“We’ve witnessed competition and conflicts among players of the region getting fiercer,” he told Yonhap news agency.
On Thursday, South Korea and China held talks on the zone, but failed to reach any agreement.
China defended its establishment of an air zone on Thursday, with a Defense Ministry spokesman telling state media it was “completely justified and legitimate”.
US Vice-President Joe Biden is expected to express America’s concerns to China when he makes a scheduled visit next week.
Joe Biden would “convey our concerns directly and… seek clarity regarding the Chinese intentions in making this move at this time”, a senior US official administration said.
The vice-president will also make stops in Japan and South Korea during his trip to Asia.
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