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A total of 50 people were arrested in connection with the annual protest organised by the Anonymous group, which sees participants wearing Guy Fawkes masks to protest against capitalism.
Police said early this morning that a number remained in custody and three officers were taken to hospital with injuries sustained during the protests, which centred around St Martin's Place, Trafalgar Square and Parliament Street.
None of their injuries are believed to be life-threatening.
A police horse also required treatment and in a separate incident, one man was arrested on suspicion of assaulting a police officer.
He remained in custody at a central London police station this morning.
An unattended police car was also set alight in Queen Anne's Gate, but police said the fire was extinguished within minutes and no officers were injured in the blaze.
On the Million Mask March Facebook page, protestors responded to the car fire and said: "We do not condone irresponsible violence.
"You might want to see the pictures across all the protest where Anonymous were chatting in a friendly way.....this was a worldwide peaceful protest."
Met officers were stationed across various parts of London including Oxford Street after being on alert of security breaches to corporate headquarters such as the British Broadcasting House in Great Portland Street.
The major crackdown came in this year after clashes took place between protesters and police last November.
Three men were also arrested after police found knives, smoke and paint grenades, gas cannisters and lock picks during a stop and search in Trafalgar Square.
They were taken to a central London police station where they remained in custody this morning.
Comedian Russell Brand took part in last year's march , during which 10 people were arrested, including three on suspicion of assaulting a police officer.
The Facebook page for this year's protest also said: "the police are not your friends".
"What's missing is accountability, anonymous believes that all living creatures should be accountable for their actions.
"2016 will see accountability.
"Police officers will be held personally accountable for their actions."
Commander BJ Harrington, of the Met Police, said: "Officers have been hospitalised, a police horse suffered injuries and a police car was criminally damaged during the course of the protest which is completely unacceptable.
"I praise the professionalism and restraint that officers have shown in the face of hostile provocation and enabled the policing operation to pass without major incidents.
"We will bring those responsible for the criminality to face justice."