“This is very sad news for Hong Kong’s autonomy and freedom,” Mr. Cohen said in a statement.

Under a formula called “one country, two systems,” Hong Kong has been allowed to run its own internal affairs and retain its culture of civil liberties — including press freedom, academic freedom, freedom of assembly and rule of law — since its return to Chinese sovereignty in 1997 after more than 150 years as a British colony.

But under President Xi Jinping, who came to power in 2012, the Chinese government has been taking a more heavy-handed approach to Hong Kong, emphasizing the “one country” part of that formula. Mr. Xi has sought to stamp out ideas that he sees as a threat to the Communist Party’s more-than-six-decade monopoly of power on the mainland, including the influence of values embraced in Hong Kong.

“Xi Jinping is determined to eradicate from China what might be called the ‘seven deadly sins’ of Western values,” Roderick MacFarquhar, a professor at Harvard University who focuses on Chinese history and politics and is currently in Hong Kong, wrote in an e-mail. “Hong Kong is a poster child for those values, and the rejection of an H.K.U. committee’s choice for pro-vice chancellor because the nominee was politically incorrect by Beijing standards is an example of the ongoing battle to whittle away those ‘sins’ where they are most flagrant.”

Fears in Hong Kong over the mainland’s growing influence came to a head last year, after the Communist Party-controlled National People’s Congress set down rules for electing the city’s top official that all but ensured that only candidates approved by Beijing could appear on the ballot. That decision prompted the demonstrations that turned parts of the city into protest camps for months.

Supporters of Mr. Chan held a candlelight vigil at the university on Tuesday night after the vote against his promotion was announced, and the news dominated local coverage the next day. A Hong Kong lawmaker, Ip Kin-yuen, a member of one of the university’s alumni associations, said in a video posted on his Facebook page that it was “the saddest day for Hong Kong University in the past 100 years.”

The council’s deliberations on Tuesday night were confidential, but Billy Fung, one of its two student representatives, released a summary of the meeting on the Internet within hours of the decision. According to Mr. Fung, committee members strongly criticized Mr. Chan, saying he was not qualified for the post because he did not have a Ph.D. or sufficient academic publications, lacked integrity and had only advanced as far as he had professionally because he was a “nice guy.”