The case prompted calls for the government to consider scrapping quarantine exemption for cargo crew.
Officials said the crew member, 36, left for the United States on Saturday and flew back to Hong Kong two days later.
Tests taken before he left Hong Kong and after his return came back negative.
He then stayed at home for most of the time for medical surveillance, except from going out to buy food briefly on Wednesday and getting tested at a mobile specimen collection station.
The test came back preliminary positive with the N501Y mutant strain detected. The man also started developing symptoms with a Ct value about 25 to 29.
Testing by the Department of Health also revealed that the spike protein gene of the patient’s sample involved T478K mutation.
“In view of the testing property of the Omicron variant, both N501Y and T478K are two of the targets to detect the Omicron variant, hence the [Centre for Health Protection] suspects at this stage that the patient carries the Omicron variant,” officials said in a statement.
Further tests are still needed to confirm if the patient carries the Omicron variant.
Authorities said residents of Cheung Hing Building on Pitt Street, where the man lives, are required to get tested before midnight, with the operation expected to be wrapped up by 7am on Friday.
Dr Joseph Tsang, an infectious disease expert, expressed concern about the policy allowing quarantine exemption for cargo crew.
“It is necessary to re-address whether it is time for us to plug this loophole because if Omicron and Covid cases leak into our community, you can imagine how fast or how rapid the Omicron variant can spread around in the community, resulting in the fifth wave of community outbreak,” he said.
Tsang also warned the emergence of such cases would hinder the reopening of the border with the mainland.
Hong Kong has so far reported nine imported cases of the Omicron variant.
Last updated: 2021-12-16 HKT 23:00