A 52-year-old man who flew in from Mauritania on Sunday was found to have the virus while in quarantine at a hotel in Tai Kok Tsui.
The other new patient was a 20-year-old man who arrived from the United Kingdom on Tuesday.
Both men had mutated strains of the coronavirus and were asymptomatic, officials said.
There were also a handful of new preliminary positive cases.
Hong Kong has recorded a total of 11,874 cases so far, with 210 deaths.