As term kicked off earlier this month, posters and banners calling for semi-autonomous Hong Kong to split from the mainland were plastered on walls and bulletin boards after a tense summer that saw pro-democracy lawmakers ousted and leading activists jailed.
Independence calls grew out of the failure of mass Umbrella Movement rallies in 2014 to win democratic reform for Hong Kong and have been fanned by growing concerns that Beijing is tightening its grip on the city.
The nascent independence movement has incensed China and local officials have also railed against activists.
When university chiefs penned a joint statement last week describing pro-independence banners as an abuse of free speech, angry students accused them of kowtowing to Beijing and censoring legitimate political debate.
"Freedom of expression is not absolute," the statement said, casting independence as contravening the city's mini-constitution, the Basic Law.
University authorities also ordered students to immediately take down banners that violated school policies.
Student unions questioned how putting a political opinion went against the Basic Law, which guarantees freedom of speech.
"Universities are supposed to be the last bastions to defend these values, but instead they became the first ones to try to control (us)," Justin Au, president of the student union at the Chinese University of Hong Kong, told AFP.
"We find it very bizarre," he added, saying he believed the move came under pressure from the government.
Student anger was also exacerbated when a pro-Beijing legislator called for the murder of independence advocates at a public rally last week, with little public chastisement from authorities.
"It shows the powerful may have more freedom of speech than ordinary citizens," said Thomas Lee, secretary at the CUHK student union.
