"Leading officials of the Foreign Ministry have summoned the US ambassador and the Japanese ambassador on separate occasions and lodged solemn representations," China's Foreign Ministry spokesman Qin Gang said in a statement.
Earlier, he told a media briefing that China expressed grave concern over the joint statement and urged Washington and Tokyo to discard their Cold War mindset.
"We have grave concerns over some of the contents in the US-Japan joint statement. It will be detrimental to the proper solution of relevant issues and the stability of the region to make indiscreet criticisms or remarks on the affairs of other countries," he said.
The US and Japan issued the statement today after Obama's visit to Japan during which he held talks with Japanese Prime Minister Shinzo Abe.
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The US-Japan security treaty, an outcome of the Cold War, cannot change the fact that the Diaoyu Islands, which Japan calls Senkakus, are China's inherent territory, he said.
No one can shake the firm will of the Chinese government and people to safeguard China's territory and sovereignty no matter what he says or what he does, Qin said.
Qin said China has indisputable sovereign rights over the islands in the South China Sea and the adjacent waters.
"China has full sincerity to peacefully solve differences and disputes via direct dialogue between parties concerned, but we will never allow any infringement of China's sovereignty and territorial integrity," he added.
Fundamentally, the fact that the US and Japan use their security treaty to cement bloc politics and undermine a third party's interests is "inappropriate and violates the basic norms guiding international relations," said Qin.