It came just hours after US Defense Secretary Jim Mattis told the security summit that China's military build-up and deployment of weapon systems in the contested sea was aimed at intimidating its neighbors.
Mattis on Saturday referred to that disinvitation as an "initial response" to China, but he did not outline any additional steps that may be taken. It was, he said, a "relatively small effect, I believe there are much larger consequences in the future".
The Chinese general, however, said Beijing's actions were aimed at "national defense".
"I believe there are much larger consequences in the future when nations lose the rapport of their neighbours. eventually these (actions) do not pay off", Mattis said. "So that's where the security threat comes from for them", said Mintaro Oba, a former US diplomat focused on Northeast Asia.
China believes islands, islets and other maritime features in the South China Sea are its sovereign territory and that it is within its rights to build defenses on them.
"Despite China's claims to the contrary, the placement of these weapons systems is tied directly to military use for the purposes of intimidation and coercion", the defence secretary said.
Mattis emphasized that the US military wants more transparency from China. China claims Taiwan as its own and it is one of its most sensitive issues.
"Make no mistake: America is in the Indo-Pacific to stay".
Senior Col. Zhao Xiaozhuo said a USA move to send two warships into China's "territorial waters" was a violation of law, and an "obvious provocation to China's national security and territorial integrity". It was not immediately clear whether that invitation would stand after the conference.
Senior Col. Zhao Xiaozhuo said a US move a couple years ago to send two warships into China's "territorial waters" was a violation of law, and an "obvious provocation to China's national security and territorial integrity".
Mr Mattis responded that the question reflected a fundamental disconnect with the way worldwide tribunals have spoken on the matter.
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Reuters first reported that two U.S. Navy warships sailed near South China Sea islands claimed by China on Sunday.
There are now about 28,500 United States troops based in South Korea.
Trump said on Friday an unprecedented nuclear arms summit with North Korean leader Kim Jong Un that the United States pulled out of will now go ahead as scheduled on June 12 in Singapore, adding another twist to a high-stakes diplomatic dance. "This is not a revisionist view", Mattis said.
Gen Mattis had made his critical comments at a security summit in Singapore.
Last week the USA withdrew an invitation for Beijing to participate the exercise known as Rim of the Pacific. China had participated in these exercises in 2014 and 2016. "It calls into question China's broader goals", Mattis said.
Beijing has begun projecting power beyond its borders, most notably through the construction and militarization of man-made islands in disputed areas of the South China Sea.
Mr Mattis said maintaining freedom of navigation in the region was...
Two U.S. warships sailed close to the Paracel Islands on May 27 in the latest freedom of navigation operation created to challenge Beijing's claims. It was the latest freedom of navigation operation created to challenge Beijing's claims. China protested the move.
In recent years, the USA had sought to stabilize military relations with China, but the militarization of the islands has been a persistent point of conflict.
The South China Sea is one of the busiest shipping lanes in the world, and rich in fish and potential oil and gas reserves.