"The government is closely monitoring the related activities with great interest, and has conveyed Japan's concerns to the Chinese side," deputy chief cabinet secretary Kazuhiko Aoki told reporters a day after the exercises around the self-ruled island.
Aoki told a regular briefing that on Sunday, two Chinese navy ships -- including the aircraft carrier Liaoning -- navigated through seas south of Yonaguni island.
Chinese jets took off and landed on the Liaoning, Aoki said, and Japanese planes "scrambled" the next day.
Japan regularly scrambles fighter jets in response to foreign aircraft near its islands.
"China in recent years has been further expanding and activating its military activities around Japan," he added.
"The government will continue closely monitoring the Chinese navy vessels' activities around Japan, and do everything we can in collecting information, patrolling and monitoring."
Relations have worsened between Beijing and Tokyo in recent years as China expands its military presence in the region and Japan boosts security ties with the United States and its allies.
A Chinese military aircraft staged the first confirmed incursion by China into Japanese airspace in August.
That was followed in September by the Liaoning sailing between Yonaguni and another Japanese island near Taiwan for the first time.
Later, a Japanese warship sailed through the Taiwan Strait for the first time, drawing an angry response from Beijing.
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