Japan protested to China over the incident but China brushed off the complaint saying the flight by the Chinese aircraft was "completely normal".
Sino-Japanese relations took a tumble in September after Japan bought the tiny islands, called Senkaku in Japan and Diaoyu in China, from a private Japanese owner.
Patrol ships from the two countries have been shadowing each other since then in a standoff that has raised concern that a collision could escalate into a clash. Yesterday's incident was the first time both sides used aircraft in the dispute.
"Despite our repeated warnings, Chinese government ships have entered our territorial waters for three days in a row," said Japanese Chief Cabinet Secretary Osama Fujimura.
"It is extremely regrettable that, on top of that, an intrusion into our airspace has been committed in this way," he said, adding that Japan had formally protested through diplomatic channels.