Tokyo denied anything was fired during the encounter, and said it had protested to Beijing over the allegation.
The two countries intermittently spar over claims of air and sea misconduct in and above the waters of the East China Sea, where they are engaged in a row over the ownership of uninhabited islands.
China did not give details about its manoeuvres, but said its aircraft had been carrying out "routine far seas training" when they passed through the Miyako Strait in the Okinawan chain.
The strait is a pinch point in Japan-China relations because it is one of the few egresses into the Pacific Ocean for Chinese ships and aircraft that avoid Japanese airspace.
Beijing's growing military is keen to flex its muscles and push further afield as it develops a "blue seas" navy capable of operating far from home waters, but is hemmed in by the Japanese archipelago.