China's Defense Ministry
said Saturday that the Japanese jets "interfered with Chinese military aircraft from close range and even launched jamming shells, which endangered the safety of Chinese aircraft and crew."
Japan said that fighter jets were scrambled when six Chinese military aircraft "trespassed" into its territorial waters in the Miyako Strait.
"It is extremely regrettable that the Chinese defense ministry announced unilaterally something that clearly differs from the fact. This damages the improvement of Japan-China relationship and we have lodged strong protest," Japan's Chief Cabinet Secretary Yoshihide Suga said Monday.
The nearby waters are home to a long-running territorial dispute between China and Japan over the Senkaku islands, which China calls the Diaoyu islands.
It's not the first time
the two countries have clashed in this way. In October, Japan said it had dispatched its warplanes 407 times between April 1 and September 30 in reaction to increased Chinese military flights near Japanese airspace.
That's almost double the number of intercepts Japan's Air Self Defense Force made on Chinese aircraft in the same period in 2015.
The flights by the Chinese People's Liberation Army (PLA) aircraft flew near waterways to the north and south of Taiwan, but did not encroach upon its air defense identification zone, Taiwan's Ministry of National Defense (MND) said.
The Chinese government has said that the mission was routine, legal under international maritime law, and that it will carry out similar excursions in the future.
It is only the second time that Chinese military aircraft have flown around Taiwan, the previous mission coming only just over two weeks ago.
On both occasions, Chinese planes flew around the Bashi Channel to the south of the island, then to the Miyako Strait, which is located north of Taiwan between the Japanese island chain of Okinawa and the Japanese-claimed Miyako Island.
Taiwan is a self-governing island that Beijing views as a "renegade province."
The long-range Chinese flights come at a time of increased tensions between Taipei and Beijing, exacerbated by US President-elect Donald Trump's questioning of the US' long-held
"one China" diplomatic policy.
The policy, in which the US recognizes Taiwan as part of China, originated with the normalization of Sino-US relations under President Richard Nixon in the 1970s.
Trump's taking of a congratulatory phone call from Taiwanese President Tsai Ing-wen broke with that protocol.
Chinese officials were furious over the first conversation in decades between a Taiwanese leader and a US President or President-elect.