The canine, which belongs to a 60-year-old woman patient, had repeatedly tested "weak positive" for the new coronavirus since Friday, when it was quarantined at an animal centre.
The city's Agriculture, Fisheries and Conservation Department (AFCD) said repeated tests suggest the dog – a Pomeranian – has "a low-level of infection".
The AFCD said experts from universities and the World Organisation for Animal Health have unanimously agreed that "it is likely to be a case of human-to-animal transmission".
The Pomeranian has not shown any novel coronavirus symptoms, it said.
New measures put in place by Hong Kong's government last Friday mean all pets infected with the coronavirus must be quarantined for 14 days. Two dogs are already in isolation.
The other dog in quarantine belongs to a second coronavirus patient that tested negative for the virus once and will be tested again before its release.
Authorities said they will continue to closely monitor the Pomeranian and return it to its owner when it tests negative for the disease.
"Apart from maintaining good hygiene practices, pet owners need not be overly concerned and under no circumstances should they abandon their pets," an AFCD spokesman said.
The financial hub has confirmed 104 cases of the new coronavirus in humans, with two deaths earlier this month.
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