The revisions to the university charters come as Beijing is grappling with anti-government protests in Hong Kong involving many students.
Changes to the charter of one of China's top universities including the dropping of the phrase "freedom of thought" and inclusion of a pledge to follow the Communist Party's leadership has sparked heated debate as well as a rare act of student defiance.
The changes to the charter of Fudan University in Shanghai, considered one of China's more liberal institutions, came to light on Tuesday when the education ministry said it had approved alterations for three universities.
Within hours, the Fudan amendments were trending on the Weibo social media platform with one hashtag viewed more than a million times.
"If I may dare to ask those who initiated the amendment of the Fudan University charter, how do you expect our generation of Fudan people to face our ancestors," said one Weibo user.
But that post and many similar ones questioning the changes, in particular the removal of "freedom of thought", was deleted by Wednesday afternoon although the issue was being discussed in private WeChat groups.
Since President Xi Jinping came to power in 2012, China has tightened controls on the internet and various aspects of civil society in a campaign that has seen increasing censorship and shrinking space for protests, including on campuses.
The revisions to the university charters come as Beijing is grappling with anti-government protests in Hong Kong that have involved many students.
A video circulating on Twitter on Wednesday afternoon showed a group of Fudan University students singing their college anthem, which includes the phrase "freedom of thought", during their lunch break.
Students there confirmed to Reuters that the event had taken place.
Telephone calls to Fudan University's press department to seek comment went unanswered. The Ministry of Education did not immediately respond to a faxed request for comment.
Student protests have been rare in China since the crushing of a pro-democracy campaign led by students at Beijing's Tiananmen Square in 1989.
Some of the commentators on Weibo discussed how the amendments pointed to an expansion of Communist Party control, with the revised charter saying that Fudan's "party committee is the core of the university" and would be responsible for setting its direction and making major decisions.
The new charter said the university would "weaponise the minds of teachers and students using Xi Jinping’s socialism ideology with characteristics of China in the new era”.
Fudan is ranked 109 globally in the Times Higher Education's 2020 World University Rankings.
The two other universities that made changes to their charters were Shaanxi Normal University and Nanjing University, according to documents published by the Ministry of Education, which showed that it had approved the changes on December 2.
Their revised charters similarly included references to strengthening the leadership of the Communist Party at the universities.