Marine police boats were sent to rescue the passengers, with local media saying many had injuries to limbs and faces.
Some passengers waited on board to be rescued for several hours.
"The lights suddenly went out. It was chaotic at first but then the passengers managed to calm down soon," one passenger told the South China Morning Post.
The RTHK news site said five people were still in a critical condition on Monday morning.
Hong Kong has one of the busiest waterways in the world, with the Macau route one of the most popular.
Dozens of people were injured in November in a similar incident with a ferry hitting an object in the water in 2013.
In October 2012, 39 people died in a crash between the Lamma IV pleasure boat and a passenger ferry. The ferry captain was convicted of manslaughter.
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