Riot police used batons and pepper spray and fired warning shots into the air early on Tuesday after authorities tried to move illegal street vendors from a district in the city.
Protesters hurled bricks at police as scuffles broke out, while other demonstrators set fire to rubbish bins in the streets of Mong Kok, a gritty neighbourhood across the harbour from the heart of the Asian financial centre.
A police statement said three men aged 27 to 35 were arrested for assaulting a police officer and obstructing police, while another three police officers received hospital treatment. Broadcaster RTHK said later that 24 people had been arrested.
The scuffles broke out after police moved in to clear "hawkers", or illegal vendors who sell local delicacies, trinkets and household goods, from makeshift streetside stalls.
The hawkers, a common sight on Hong Kong's bustling streets, quickly attracted a strong social media following under the hashtag #FishballRevolution.
Hong Kong Chief Executive Leung Chun-ying told reporters at a news conference that the city's government strongly condemned the violence.
Secretary for Security Lai Tung-kwok said police were investigating "indications" that the clashes had been organised. When asked about the warning shots, Lai said police had taken all necessary actions.
The unrest underscores how tensions remain unresolved more than a year after the end of pro-democracy protests in the city.
Mong Kok, a popular and densely populated shopping and entertainment district, captured world headlines for 11 weeks in late 2014 when it was occupied by activists demanding greater electoral freedom from Beijing.