The row over the Beijing-backed centres -- which number nearly 100 in the US, mostly on the campuses of publicly-funded state universities -- comes after a number of US, Canadian and other schools publicly cut ties with them.
Chinese foreign ministry spokeswoman Hua Chunying described Confucius Institutes as "a bridge linking China with the rest of the world" and maintained that all activities at the centres were "open and transparent".
"We hope that all countries can make joint efforts to discard prejudice and build the bridge of friendship much stronger," she added.
On Thursday, Congressman Chris Smith, who sits on the US House of Representatives foreign affairs committee, voiced concern that the institutes are muting criticism of Chinese authorities.
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"Is American higher education for sale?" said the New Jersey Republican, a longtime critic of China's Communist authorities who also co-chairs the Congressional-Executive Committee on China.
In recent months, several colleges and universities have broken ties with Confucius Institutes over concerns about their impact on free expression.
The University of Chicago, which has had a Confucius Institute since 2009, announced in September that it was suspending talks on a renewal of the centre's contract. More than 100 professors had signed a petition urging the school to shut the centre.
Days later Pennsylvania State University announced that it would close its Confucius Institute by the end of the year. Canada's McMaster University, the University of Sherbrooke and the Toronto District School Board have made similar decisions.
Critics contend that the institutes present a whitewashed view of Chinese history and that administrators who accept Chinese funding do so with an implicit understanding that discussion of certain sensitive topics -- such as Taiwan, Tibet or the Tiananmen Square crackdown -- is off-limits.
Those opposed to the centres also point to instances of discrimination in their hiring practices. McMaster last year faced a complaint from a former teacher who was an adherent of the Falun Gong spiritual movement, which is banned in China.