More than 40 Chinese military aircraft on Sunday traversed the Miyako Strait between Japan's Miyako and Okinawa Islands, to carry out training in the West Pacific, according to a statement on China's defence ministry website.
The Sukhoi Su-30 fighters, bombers and refuelling aircraft did not violate Japanese airspace.
Japan's defence ministry said it was the first time Chinese fighters had passed over the strait.
The drill is aimed at "testing far sea combat capabilities", the Chinese statement said. It follows China's first military flight, carried out by spy planes, over the Miyako Strait last year.
Beijing asserts sovereignty over almost all of the South China Sea, dismissing rival partial claims from its Southeast Asian neighbours. It rejects any intervention by Japan in the waterway.
In recent months Japanese Prime Minister Shinzo Abe has criticised China for rejecting a July ruling by an international tribunal, which said Beijing's extensive claims to the waters had no legal basis.
That dispute relates to uninhabited islets controlled by Japan known as the Senkakus in Japanese and the Diaoyus in Chinese.
Abe said today Japan would "never tolerate attempts to unilaterally change the status quo" in the disputed waters, or "wherever else in the world", in an apparent response to the Chinese move.
"We pledge to protect Japan's territory, and in the sea and air," he said in a speech to open a new parliamentary session.
In its statement the Chinese defence ministry said it had also mobilised an unspecified number of bombers and fighters to patrol the East China Sea Air Defence Identification Zone (ADIZ).
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