One of the patients is a 31-year-old domestic helper from the Philippines, whose infection triggered the overnight lockdown of a building in Happy Valley.
About 130 residents were tested and no positive cases were found.
The helper had received the Johnson & Johnson single-shot vaccine, and she tested positive after leaving quarantine.
The other two patients, who arrived from Canada and Pakistan via Turkey, have been fully vaccinated and were in hotel quarantine.
One of them carried the L452R mutant strain and the other the N501Y strain.
Hong Kong has recorded 12,399 Covid-19 infections so far.