The Glory Sky, a cargo ship, arrived in the territory from Japan on Wednesday.
Officials say the 51-year-old Covid patient and his colleagues did not come ashore, and no local people boarded the boat.
The man accounted for one of three new imported Covid cases on Friday. The other two patients recently flew in from South Korea and the United States.
Meanwhile, the government says that from Monday, it will refuse entry to non-Hong Kong residents who’ve been to Singapore or Iceland in the past three weeks, because Covid cases with the Omicron variant have been detected there.
It says these countries will be listed as Group A, or high-risk places, as a preventive measure.
Hong Kong residents who’ve been there can only board a return flight if they can present a recognised vaccination record, and they’ll be subject to several Covid-19 tests during and after a three-week quarantine.
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Last updated: 2021-12-03 HKT 20:40