Riot police equipped with masks and shields swarmed towards protesters who fled following a tense standoff close to a ferry terminal on the main island.
In a separate incident, unidentified masked men, many wielding sticks, attacked anti-government protesters inside a Hong Kong station on Sunday night.
A live Facebook broadcast byshowed the men charging into a crowd of protesters in Yuen Long, a district in the city's northwest, close to the border with China.
Thousands of anti-government demonstrators had earlier taken to the streets of Hong Kong for the seventh weekend in succession to express their anger at the growing influence of Beijing in the semi-autonomous territory.
The city has been plunged into its worst crisis in recent history by weeks of marches and sporadic violent confrontations between police and pockets of hardcore protesters.
The initial protests were sparked by a now-suspended bill that would have allowed extradition to mainland China.
The movement has since evolved, with protestors calling for democratic reforms, universal suffrage and a halt to the erosion of freedoms in Hong Kong.
Police have fired tear gas and rubber bullets, while the parliament has been invaded by protesters as Beijing's authority faces its most serious challenge since Hong Kong was handed back to China in 1997.
Under the 1997 handover deal with Britain, China promised to allow Hong Kong to keep key liberties such as its independent judiciary and freedom of speech.
But many say those provisions are already being curtailed, citing the disappearance into mainland custody of dissident booksellers, the disqualification of prominent politicians and the jailing of pro-democracy protest leaders.