Xinhua termed Trump's language was "racist and xenophobic", revealed "politicians' irresponsibility and incompetence", and risked increasing fears over the virus.
Hours before the Trump's tweet, Secretary of State Michael Pompeo told top Chinese diplomat Yang Jiechi the Trump administration strongly objects to China's "efforts to shift blame" for the coronavirus to the USA, according to a State Department readout.
There was also criticism from within the United States, with New York's Mayor Bill de Blasio saying the phrase risked "fuelling more bigotry" against Asian-Americans.
The jury is still out on whether the world's second most populous nation can hold off the coronavirus pandemic, but so far at least, India has kept things at bay, The New York Times reports. Last week, outspoken official Zhao Lijian from China's ministry of foreign affairs accused the U.S. military of bringing the virus to Wuhan.
But China has sought to distance itself from the virus, saying the origin is still unknown, while seeking global goodwill by offering aid to countries facing serious outbreaks.
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Trump tweeted about the "Chinese Virus" Tuesday night.
Separately, the State Department on Friday summoned the Chinese ambassador, Cui Tiankai, to register its protest over Beijing's seeming attempts to promote a conspiracy theory.
Meanwhile, Beijing, who has been accused of covering up the initial outbreak, has allowed disinformation surrounding the virus to spread in recent days, with foreign ministry spokesman Zhao Lijian perpetuating one conspiracy theory in tweeting last week that "it might be United States army who brought the epidemic to Wuhan".
After the Wuhan outbreak, China built 14 new hospitals, including two in the city, within weeks in the last two months to provide thousands of beds for the infected as the epidemic spread rapidly. "We are very angry and strongly oppose it [the tweet]". Make public your data!
According to China's official Xinhua news agency, Yang in his conversation with Pompeo, issued a "stern warning to the United States that any scheme to smear China will be doomed to fail". "The U.S. side should immediately correct its mistakes and stop making groundless accusations against China", read the statement.