The march, which began peacefully in the central neighbourhood of Tsim Sha Tsui, also called for reforms to the Hong Kong Police Force which has been accused of using violent tactics to diffuse protests, reports Efe news.
Just after 4.30 p.m., chaos seized the financial hub when radicals began to block roads, attack the police station and vandalize ATMs and subway stations.
"In response to the rioter's illegal acts, police are now using the minimum force necessary, including the Specialised Crowd Management Vehicle, to disperse rioters along Nathan Road," the Hong Kong police tweeted.
"We warn the rioters to stop their illegal acts immediately," the tweet continued.
Police advised members of the public to keep windows closed, stay indoors and avoid travelling to the affected area.
The police force justified its decision to ban Sunday's march saying that these types of concentrations tend to degenerate into violent incidents.
After police deployed water canons in the area, a video shared by Hong Kong Free Press on Twitter showed protesters helping to remove stains from the water canon dye on a Tsim Sha Tui Mosque.
On Friday, the police rejected an application for the Sunday march called by the Civil Human Rights Front against the Carrie Lam-led government's anti-mask ban, the South China Morning Post reoirted.
In its letter of objection, the police cited violent incidents stemming from earlier protests.
The force has refused three other applications by the front in the past three months, on similar grounds.
On all occasions, thousands marched on despite the bans.
Apart from echoing the main demands of the protest movement, which has been continuing since June, the front also called on the government to abolish the anti-mask law it brought it earlier this month.
The law stipulates a penalty of jail for up to one year and a fine up to HK$25,000 ($3,200) for wearing any face covering at a public gathering.
( With inputs from IANS )