Pictures showed wounded people being stretchered off the boat, some wearing oxygen masks, onto a pier in Hong Kong's central financial district to waiting ambulances.
Authorities received a call at around 6:00pm local time (1000 GMT) warning the ferry carrying 163 passengers and 11 had lost power after an accident off Siu A Chau, near the larger island of Lantau.
"So far it is understood around 100 people have been injured," a government spokesman said in a statement emailed to AFP.
An AFP reporter on the scene later saw some 20 ambulances waiting near Government Pier as passengers gave statements to police.
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Passengers were quoted in local reports describing chaos as the boat lost power, leaving wounded people stumbling around in darkness.
"It went dark. A lot of people were injured and many were bleeding," one man with a bandage on his head told Apple Daily.
The accident happened when the high-speed ferry hit an "unidentified object" in the water, according to the ferry's operator Shun Tak.
A subsequent inquiry found a "litany of errors" contributed to the accident, the city's worst maritime disaster for over 40 years.
The tragedy shocked the Asian financial hub, one of the world's busiest ports, which had prided itself on its good safety record.
Last June, more than 50 people were injured when a Macau-bound ferry crashed into a seawall off the coast of the gambling enclave.