British journalist Victor Mallet, who was trying to enter on a tourist visa, was turned away at the border after several hours of questioning by immigration officers, the Financial Times reported late on Thursday.
Mallet did not comment further when contacted by Reuters.
The group said it was "deeply concerned with this action, taken with no stated or apparent legal basis" in the first incident of its kind against a journalist since Hong Kong returned to Chinese sovereignty in 1997.
Mallet was denied a work visa renewal in October without explanation, although it is widely believed to have been punishment for chairing a talk with a pro-independence activist at the Foreign Correspondents' Club (FCC) in August.
The denial comes just a month after the territory refused to renew his work visa without explanation.
Analysts have cited the FT editor's case among other examples of Hong Kong officials taking a tough line on perceived critics and dissent in the former British colony.
Hong Kong International Literary Festival said late on Thursday it had found a new venue for the talks, the Annex event and exhibition space in the Central district of Hong Kong island, adding that it "stands by the principles of free speech and cultural expression".
Authorities did not give a reason for the visa decision, which shocked many in the city's worldwide community and revived a debate over promised freedoms in the financial hub.
"Refusing a visa in this case, to a bona fide journalist working for one of the world's leading newspapers, sets a awful precedent for Hong Kong's reputation as a place where the rule of law applies and where freedom of speech is protected by law", it said in a statement on its website.
On Thursday, exiled Chinese author Ma Jian tweeted that the Tai Kwun arts centre, which was set up with government support, had cancelled two events where he was to speak.
Ma responded on Twitter saying he was a "novelist not an activist" and was simply attending the festival to discuss his new work.
Tai Kwun director Timothy Calnin said in an emailed statement that the centre "did not want to become a platform to promote the political interests of any individual".
Ma said he had been unable to find a Hong Kong publisher for his satirical novel, China Dream, dubbed by Hong Kong's literary festival organisers as "Ma's answer to President Xi Jinping's goal of restored national greatness". "Without them, life has no meaning".
Ma is due to arrive in Hong Kong on Friday afternoon.