Protests have gathered pace since the appointment of a liberal law scholar to a senior administrative post at HKU was rejected last week.
The university's council, which has a number of members seen as pro-Beijing, voted against Johannes Chan becoming pro-vice chancellor.
Some members of the council, HKU's top decision-making body, are appointed by the city's unpopular leader Leung Chun-ying.
Chan was a close colleague of pro-democracy leader Benny Tai, also an academic at HKU. Tai helped orchestrate last year's mass pro-democracy protests which brought parts of the semi-autonomous Chinese city to a standstill.
Some were wearing t-shirts with the Martin Luther King quote: "Nothing in the world is more dangerous than sincere ignorance and conscientious stupidity."
"We should ask whether the government is trying so hard to destroy Hong Kong's tertiary education that it doesn't care about the consequences," education lawmaker Ip Kin-yuen told reporters.
"It's a threat to Hong Kong as a whole."
Wednesday saw 2,000 students, professors and alumni gather at the HKU campus for a silent march.
On Thursday, academic staff from across the city's universities and higher education institutions launched a new group -- the Scholars' Alliance for Academic Freedom (SAAF).
"Academic freedom can only exist through perpetual awareness, insistence and collective work," it said in a statement.
"We are aware of the storm and the darkness that awaits us; we have no choice but to face it head on and walk against the wind."
Anger was stoked further today after reports in local media that Leung had met with HKU vice-chancellor Peter Mathieson in August and September, ahead of the decisive council meeting.
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