Police later confirmed in a statement that an officer discharged his revolver and shot a person.
The incident marks the third time a protester has been shot with a live round since protests broke out in June over a now-withdrawn extradition bill.
A video circulating online showed what appeared to be a police officer shooting a protester at close range in the chest that morning in a video circulating online. The protester, who looks unarmed, then slumps to the ground.
The shooting spurred online speculation that restrictions on officers using firearms were relaxed in order to curb Monday’s strike, but police denied this in a statement.
"Online rumours stated that Police management have ordered frontline officers to recklessly use their firearms in today’s operations," the statement read.
"Police clarifies that this allegation is totally false and malicious. Police has strict guidelines and orders regarding the use of firearms."
The strike was meant to call attention to the death of a student protester, which many residents believe was indirectly caused by police as they dispersed an illegal assembly last week.
Protesters began building barricades on major thoroughfares and vandalizing tunnel entry points around 7 am (2300 GMT on Sunday) in a bid to prevent commuters from travelling to work.
In the Sai Wan Ho district, where the shooting occurred, angered residents and protesters set up barricades, lit fires, and vandalized a metro station. Police fired tear gas and pepper spray in response.
Police also fired tear gas in Central, the heart of Hong Kong’s financial district, where many office workers without gear had assembled on Monday to strike in solidarity with black-clad anti-government protesters.
Another video circulating online shows a man arguing with people with anti-government views being set on fire by a protester. He is being treated at a nearby hospital according to the South China Morning Post.
By midday, train lines and buses were crippled by the disruptions, with suspensions on eight of the territory's 11 train lines, according to the city's transport app.
Police said in a statement that protesters threw petrol bombs into a train carriage for the first time. The carriage appeared to be empty in video footage of the incident.
Classes were cancelled at multiple universities after tear gas was deployed at the Chinese University of Hong Kong and the Hong Kong Polytechnic University, according to local media.
Protesters also infiltrated malls as the strike is also meant to coincide with Singles' Day, China's anti-Valentine's Day holiday where single people are encouraged to buy themselves gifts.
The Hong Kong protests erupted in June over a now-suspended extradition bill that would have allowed Hong Kong residents to be extradited to China.
The demands of the movement later grew to include universal suffrage and an independent inquiry into police violence against protesters.
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