The incident, which involved a cargo ship and a container vessel, happened in the early hours of May 5 near Po Toi Island, reports said.
The cargo ship is believed to have sunk with its 12-member crew on board. One man was rescued by a fishing boat.
Chinese officials are now conducting a search and rescue mission.
The mission was being co-ordinated by the Guangdong Maritime Rescue Co-ordination Centre and Hong Kong had also sent rescue boats and a helicopter to the area, the South China Morning Post newspaper said.
China was sending more than a dozen ships and at least three helicopters to the area, state-run Xinhua news agency said.
The rescued crew member was in hospital suffering minor injuries, a police official told AFP news agency.
Hong Kong is one of the world’s busiest ports and has a relatively strong safety record.
Hundreds of vessels, from commuter ferries to container ships, ply its waters daily
Last year, about 85 people were injured when a high-speed ferry near the island of Hei Ling Chau hit what officials said was an unidentified object.
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