By Agence France-Presse
Rights groups and media organisations said the decision was unprecedented and highlighted growing threats to Hong Kong's cherished freedoms from Beijing.
Victor Mallet, the FT's Asia news editor, earned the ire of authorities for hosting a speech by Andy Chan, the leader of a tiny pro-independence political party.
Chan attacked China as an empire trying to "annex" and "destroy" Hong Kong in a strident speech at the city's Foreign Correspondents' Club, where Mallet serves as vice president.
China's foreign ministry had requested the club to pull the talk, but the FCC refused, arguing that all sides of a debate should be heard.
Rival protesters picketed the lunchtime event and the city's former leader Leung Chun-ying called for the club to be evicted from its government-owned premises.
"This is the first time we have encountered this situation in Hong Kong," said the FT, in a statement confirming the British citizen had been denied a visa renewal.
"We have not been given a reason for the rejection."
Hong Kong's last British governor Chris Patten said the move was a "serious blow against free speech" as well as defying the promise of a high degree of autonomy made to the city when it was handed back to China by Britain in 1997.
"The Hong Kong and Beijing authorities should think again and fast," Patten told AFP.
The FCC demanded an explanation from the government for what it called an "extraordinary move".
"In the absence of any reasonable explanation, the FCC calls on the Hong Kong authorities to rescind their decision," the club said.
Hong Kong's immigration department declined to comment on Mallet's case.
- Downward spiral -
Semi-autonomous Hong Kong enjoys freedoms unseen on the mainland, including freedom of expression which are protected by a handover agreement between China and Britain.
But the space for dissent is shrinking as Beijing flexes its muscles.
Hong Kong authorities last week banned Chan's Hong Kong National Party, calling it a threat to national security.
It was the first ban on a political party since 1997.
Mallet's visa denial indicated a "quickening downward spiral for human rights in Hong Kong", said Human Rights Watch senior researcher Maya Wang.
"The Hong Kong government is now following Beijing's leads in acting aggressively towards those whose views the authorities dislike."
Taiwan's Mainland Affairs Council, which deals with its China relations, said it was aware of suggestions that Mallet's visa had not been renewed because of his link to Chan's speech at the FCC and warned the move would "further suppress Hong Kong's freedom of the press and freedom of speech'.
A string of incidents including the disappearance of five Hong Kong booksellers and the ousting of six elected opposition lawmakers in recent years have fuelled concern that Chinese authorities are undermining freedom in Hong Kong.
Pro-democracy lawmaker Claudia Mo said the Hong Kong government's "vindictive" actions towards Mallet would further dent the city's reputation for a free press.
"Hong Kong is like a sinking boat, going down fast," she said.