A unit of six F-15 fighter jets was scrambled from the main island of Okinawa Prefecture after the surveillance aircraft, belonging by the Chinese Oceanic Administration, was sighted close to Uotsuri Island at 11:06 am (2:06 am GMT).
The Senkaku islands, as they are known in Japan, are presently controlled by Tokyo, but are claimed by both China, which marks them on its maps as the Diaoyu islets, and Taiwan.
The territorial dispute has been a periodic thorn in the side of Japan’s relationships with its neighbours since deposits of oil and natural gas were discovered beneath the seabed around the islands in the 1970s. Beijing and Taipei both insist that their claims are historic and that Japan illegally occupied the islands in the late 19th century.
The issue was once again brought to a head in April this year when Shintaro Ishihara, then the governor of Tokyo, announced that he was planning to purchase the islands from their private owners and administer them from the Japanese capital.
The outcry was immediate and violent, with Japanese businesses and nationals attacked in cities across China.
To thwart the nationalist governor’s plans, the Japanese government stepped in and purchased the islands, although Beijing and Taipei continue to demand talks over the sovereignty of the territory.
China has dispatched maritime survey vessels and warships to waters around the islands on an almost daily basis since the summer. The ships have entered Japanese territorial waters on 17 occasions and, when challenged, have claimed to be operating legitimately within Chinese territory.
On Thursday morning, four Chinese patrol vessels entered Japanese waters close to Uotsuri Island at around 9.10 am (12.10 am GMT), according to the Japan Coast Guard.
An over-flight of the islands by a reconnaissance aircraft - the first violation of Japanese airspace by a Chinese government aircraft since at least 1958, according to the Ministry of Defence in Tokyo - is a significant escalation of the Beijing’s actions.
It also coincides with the 75th anniversary of the Nanjing massacre. Memorial events were held in the former Chinese capital for the victims of the rampage by troops of the Imperial Japanese Army in 1937, although the two nations still differ significantly on the number of people who died.
China estimates that more than 300,000 died in the six-week period after the fall of the city, although Japanese academics claim the figure was between 20,000 and 200,000. Nationalists here insist that even the lower figure has been inflated by Chinese propaganda - making the entire episode another bone of contention.
Immediately after the Chinese aircraft had been identified over the Senkaku islands, by a Japan Coast Guard patrol vessel, Tokyo filed an official protest with Beijing.
Osamu Fujimura, the chief cabinet secretary, told reporters in Tokyo that the incident was “extremely deplorable.”
“We are determined to deal firmly with action that violates our country’s sovereignty, in accordance with domestic laws and regulations,” he said.
Radar operated by Japan’s Self-Defence Forces failed to detect the aircraft, the Defence Ministry has admitted, with Yoshihiko Noda, the prime minister, ordering government agencies to increase their surveillance and warning capabilities.
Han Zhiqiang, the acting Chinese ambassador to Tokyo, was summoned to the Foreign Ministry later in the day to receive an official protest, although the ambassador declined to accept the protest and replied that the islands are Chinese territory.