"The Japanese side openly attempted to create 'one China, one Taiwan' under the pretext of disaster relief and condolences," Chinese foreign ministry spokesperson Geng Shuang was quoted as saying by state-run Xinhua news agency.
Responding to a question, he said some senior Japanese officials sent condolences to Taiwan politicians addressing them by their "so-called official titles".
He said such a move went against the 'one-China' principle as well as Japan's commitment on the Taiwan issue, adding that China was strongly dissatisfied and had lodged representations to Japan.
Geng said the Chinese mainland was concerned after the magnitude 6.5 earthquake that hit Taiwan late on Tuesday.
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Zhang Zhijun, head of the Taiwan Affairs Office of the State Council, expressed sincere regards to Taiwan compatriots, and pledged to send rescue teams and aid.
As of today, 10 people have been confirmed dead in the earthquake which struck Taiwan's Hualien County.
The dead included four from the Chinese mainland. A total of 276 people were injured.