The skirmishes lasted for about four hours in the bustling Mong Kok neighborhood, the most turbulent of three protest sites that have snarled swaths of the city.
Police said they attempted to arrest a man who was shining his cellphone light into officers' eyes, and demonstrators responded by surging at police lines.
The two sides ended up in a tense standoff, with several protesters taunting police.
Police said they arrested three people in the confrontations, which left at least one protester bleeding from the head.
Several demonstrators arrived in Mong Kok wearing masks with the grinning likeness of Guy Fawkes, a co-conspirator in a plot to blow up the English Parliament building in 1605. Young protesters worldwide have taken up wearing the mask at demonstrations since it was featured in the 2006 film "V for Vendetta."