The drone was spotted off Japan's Yonaguni, an island where Tokyo is planning to deploy missiles in a move that has angered Beijing.
"We confirmed that an unmanned aerial vehicle believed to be Chinese, passed between Yonaguni Island and Taiwan on Monday," Japan's defence ministry said on X.
The regional Japan Air Self-Defense Forces "scrambled aircraft" in response, it said.
Beijing-Tokyo relations have soured this month, following remarks by Japanese Prime Minister Sanae Takaichi suggesting that Tokyo could intervene militarily in any attack on Taiwan.
The row escalated again on Monday when China slammed Japan's decision to push ahead with the planned deployment of missiles on Yonaguni following a visit to the island by Defence Minister Shinjiro Koizumi.
China's foreign ministry said the plan was a "deliberate attempt to create regional tension and provoke military confrontation".
Koizumi pushed back on Tuesday, saying "the medium-range surface-to-air guided missiles planned for deployment are defensive equipment intended to counter aircraft and missiles invading our nation".
"They are not intended to attack other countries, are deployed throughout Japan, and clearly do not heighten regional tensions," he told reporters.
Since 2016, the island of Yonaguni has hosted a base for Japan's army, the Self-Defense Forces, which was established despite initial objections from residents.
Tokyo had previously announced plans to deploy the Type 03 Medium-Range Surface-to-Air Guided Missile to defend the island against incoming air-to-ground missiles and aircraft.
China claims democratic Taiwan as part of its territory and has threatened to use force to bring the self-ruled island under its control.
Taiwan on Monday said that Japan's strengthening of military facilities on Yonaguni "helps maintain security in the Taiwan Strait".
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