Victor Mallet, the FT's Asia news editor and a British national, angered authorities in Beijing and Hong Kong by hosting a speech at the city's press club by Andy Chan, the leader of a tiny pro-independence political party.
Chan's party has since been banned as Beijing cracks down on any pro-independence sentiment in the semi-autonomous city.
Last week it emerged Mallet's application for a renewal of his work visa had been rejected by Hong Kong immigration authorities.
On Monday the FT said Mallet had only been granted a seven-day visitor visa after returning to the city from a trip on Sunday.
Sources with direct knowledge of the situation told AFP that Mallet was questioned at immigration and was refused automatic entry.
British citizens are usually allowed into Hong Kong without a visa and are permitted to stay for 180 days under immigration rules.
The FT said immigration officials had provided no explanation for the shortened visitor visa.
"We continue to seek clarification from the Hong Kong authorities about the rejection of his work visa renewal," said the paper, which has its regional headquarters in Hong Kong.
The FT's editorial board had earlier described the decision to refuse Mallet a work visa as sending a "chilling message to everyone in Hong Kong".
- Lawyers hit back -
In a strident speech in August at the city's Foreign Correspondents' Club (FCC), where Mallet serves as vice president, independence activist Chan attacked China as an empire trying to "annex" and "destroy" Hong Kong.
China's foreign ministry had asked the club to pull the talk, but the FCC refused, arguing that all sides of a debate should be heard and that it hosted a variety of speakers, including Chinese officials.
Britain and the United States have expressed concern over the visa refusal and its impact on press freedom.
On Monday, a group of the city's most influential lawyers also hit back.
"Such rejection calls for an explanation in light of its unprecedented nature and its profound impact on Hong Kong's press freedom," 30 lawyers said in a statement.
The group makes up the legal subsector of the electoral committee that chooses the city's leader.
Another legal organisation, the Progressive Lawyers Group, said: "Any forced retreat of foreign media outlets would be a tragic loss for Hong Kong and must be vigilantly guarded against".
A journalists' alliance handed over petitions with more than 15,000 signatures to the government Monday calling for an explanation of its visa rejection.
Hong Kong authorities have said they cannot comment on Mallet's case.
China's foreign ministry has said it supports Hong Kong "in handling the related matters in accordance with law", and warned other countries not to interfere.