He tried to enter as a tourist on Thursday but was turned away after questioning by immigration officials.
The denial comes just a month after the territory refused to renew his work visa without explanation.
In August Mr Mallet hosted an event at Hong Kong’s Foreign Correspondent Club (FCC) that featured an independence activist, drawing anger from officials.
China’s foreign ministry had urged the club to cancel the event featuring activist Andy Chan, founder of the Hong Kong National Party.
British citizens are usually allowed entry to Hong Kong for 180 days without a visa, according to the tourist board.
The FCC has reiterated its request for an explanation from Hong Kong’s top official Carrie Lam about the original visa denial.
— FCC, Hong Kong (@fcchk) November 9, 2018
Under the so-called “one country, two systems” formula, Hong Kong enjoys a high degree of autonomy and certain freedoms not available in China.
However, there are fears some of these freedoms are being eroded.
On the same day Hong Kong denied Mr Mallet entry, Chinese author Ma Jian announced the cancellation of his events in the Hong Kong International Literary Festival being held at the government-backed Tai Kwun arts complex.
Organisers will now have to find an alternative venue, he said, although it is unclear whether the events will take place at all.
As he boarded a plane bound for Hong Kong, he expressed concerns he might not be allowed through immigration, but has since tweeted that he has been granted entry.
I was let through. No problem. Just heard that the second venue has pulled out of hosting my talks.
— 马建 Ma Jian (@majian53) November 9, 2018
These latest moves come after the authorities banned the small Hong Kong National Party that advocates for the territory’s independence.
It marked the first time the territory banned a political party since it was returned to China from the UK in 1997.