Protesters were knocked to the ground by hundreds of police, some with batons, pepper spray and shields. Officers also tore down barricades around an underpass outside the government's headquarters.
The clashes worsened an already bitter standoff between authorities and activists who have taken over key roads and streets in the city to press for democratic reforms.
"Hong Kong police have gone insane today, carrying out their own punishment in private," said pro-democracy lawmaker Lee Cheuk-yan. "Hong Kong's values and its rule of law really have been completely destroyed by police chiefs."
Protester Ken Tsang said he was kicked while he was "detained and defenseless." He added that he was assaulted again in the police station afterward.
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Tsang, a member of a pro-democracy political party, lifted his shirt to show reporters injuries to his torso and said he is considering legal action against police.
Police spokesman Steve Hui said seven officers who were involved have been temporarily reassigned, and that authorities will carry out an impartial investigation. Police arrested 45 demonstrators in the clashes, and said five officers were injured.
A front-page editorial Wednesday in the People's Daily, the ruling Communist Party's mouthpiece, condemned the protests and said "they are doomed to fail."
"Facts and history tell us that radical and illegal acts that got their way only result in more severe illegal activities, exacerbating disorder and turmoil," the commentary said.