BEIJING — Students at a prominent Chinese university on Wednesday staged protests against efforts by the ruling Communist Party to further extend its control over university campuses, a rare and risky rebuke that highlighted broader concerns about the erosion of free speech under President Xi Jinping.

The protests were a response to the decision this month by Fudan University, a Shanghai institution known for its relatively tolerant culture, to rewrite its charter to emphasize loyalty to the party over traditional values like independence and academic freedom.

Fudan was one of three universities to make the changes, which were widely publicized on Chinese social media sites this week, prompting a backlash that extended beyond university campuses.

Many people criticized the universities for appearing to back away from principles they said were necessary for China to have a competitive education system. As criticism mounted, the authorities moved swiftly to limit the discussion, censoring comments and a hashtag about the issue.

The changes to the charters revived concerns that Mr. Xi, who has led a broad crackdown on free speech since rising to power in 2012, is intensifying efforts to turn universities into party strongholds and silence dissent.

“We want to show that we cannot tolerate this,” said a Fudan undergraduate who was among dozens of students protesting on Wednesday against the school’s decision to remove a reference to “freedom of thought” from its charter. The undergraduate asked to be identified only by a surname, Qiu, for fear of being punished.

While universities have never had total autonomy since the founding of the People’s Republic of China in 1949, the government has in recent decades granted them limited freedom to debate ideas, such as constitutional law, that might otherwise be shunned in official circles.

Under Mr. Xi, the space for free inquiry has rapidly narrowed. Schools have fired dissident teachers, recruited students to act as classroom informers and banned some Western textbooks. The government has also ordered schools to start research centers devoted to Mr. Xi’s signature ideology, known as “Xi Jinping Thought.”

The Communist Party has long kept a close watch on universities, especially in the aftermath of pro-democracy protests near Tiananmen Square three decades ago, which involved large numbers of students.

Now, with young people playing a pivotal role in the monthslong antigovernment protests in Hong Kong, including recent violent clashes with the police on university campuses in the semiautonomous territory, concerns about the ideological purity of students have resurfaced at the highest levels of the party.

Wu Qiang, a political analyst in Beijing, said the Hong Kong protests had underscored for the party that it should not “leave blind spots on campus.” He said that other mainland universities were likely to adopt similar statements of support to send the message that the party is “the absolute leader” of schools.

The protests on Wednesday were relatively small in size, but were risky in a country where criticism of the party and its policies can be met with serious punishment. The authorities have in recent years detained or harassed students for organizing political protests and punished professors who speak critically of the party.

The student protesters on Wednesday avoided directly attacking the party, and the authorities did not immediately intervene.

At Fudan, students gathered in a cafeteria and joined in a rendition of Fudan’s official anthem, which includes the “freedom of thought” phrase that was deleted from the school’s charter.

Several professors at the university, which was founded in 1905, posted messages online criticizing the decision to revise the charter, saying that the school should have consulted the faculty and the students. Many of their posts were quickly deleted by censors.

Sun Peidong, an associate professor of history at Fudan, said in an interview that the changes formalized the strict limits on free inquiry that have been in place at the university over the past several years.

“We don’t have to pretend anymore,” she said.

An anonymous graduate of Fudan circulated an open letter on Wednesday on WeChat, a messaging app, calling on the university to reverse course. “I earnestly hope that Fudan University can be less groveling, flattering, ingratiating, and be kindly and smartly a tower of strength,” said the letter, which was quickly removed from the internet.

Fudan officials defended the changes to the charter, calling them legal, and said in a statement that they were meant to “highlight the party’s overall leadership in school work.”

Two other schools also recently revised their charters, Nanjing University in eastern China and Shaanxi Normal University in northwestern China, adding vows to “maintain the comprehensive leadership of the Communist Party.”

A spokesman for the Chinese Ministry of Education, which this month approved the charter revisions, did not immediately respond to an email seeking comment.

Some experts have warned that China’s growing restrictions on academic freedom could undermine its efforts to attract talent and build a world-class university system, as Mr. Xi has promised.

Michael D. Swaine, a senior fellow at the Carnegie Endowment for International Peace in Washington, said revising the university charters would ultimately be counterproductive.

To survive in the long term, he said, the Community Party will need to find new ways to promote economic growth rather than “just doubling down on Leninist norms.”

Wang Yiwei contributed research.