The accident happened about 300 kilometers south of Hong Kong.
The Flying Service has not given the name or origin of the ship.
It said in a statement that crew members were negotiating difficulties caused by severe Tropical Storm Chaba, which had winds of 110 kilometers per hour.
The storm made landfall on Saturday in the western part of coastal Guangdong province.
The Hong Kong service sent two fixed-wing aircraft and four helicopters to the rescue effort.
Hong Kong authorities warned of the typhoon during the long-awaited visit of Chinese leader Xi Jinping on Thursday.
The grand opening of a new Hong Kong Palace Museum, to coincide with the 25th anniversary of the transfer of the city from British to Chinese rule, was postponed until Sunday due to the storm.
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