Police officers used batons to control the crowd, after bottles and water were thrown by demonstrators massed in Trafalgar Square.
The Met Police said the protest was being shut down because the crowd was not complying with social distancing rules and warned fines would be issued.
Thousands had gathered in central London to protest against the latest government rules, with very few wearing masks.
Officers penned the crowd in Trafalgar Square as water and bottles were thrown at them by demonstrators – with some chanting “pick your side”.
Police removed sound equipment and used batons against protesters, leaving some with visible injuries. Several protesters were led away in handcuffs.
The majority of demonstrators in Trafalgar Square have now been dispersed by police but the Met said some had moved to Hyde Park.
Demonstrators were asked to leave and the force said anyone who stayed could be subject to enforcement.
In a statement, the Met said: “Crowds in Trafalgar Square have not complied with the conditions of their risk assessment and are putting people in danger of transmitting the virus.
“This has voided their risk assessment and we have informed the event organisers they are no longer exempt from the regulations.
“By leaving now, you can keep yourself safe and avoid any enforcement action being taken by officers,” the statement added.
The “we do not consent” rally came a week after a separate event which saw more than a dozen officers injured when a “small minority” targeted police and more than 32 arrests were made.
Commander Ade Adelekan, who is leading the Met operation, previously said that while there was “great frustration” at the regulations, they were designed to keep people safe from the virus.
“By flagrantly gathering in large numbers and ignoring social distancing, you are putting your health and the health of your loved ones at risk,” he said.
He added that he would not tolerate police being targeted during protests and officers would “respond quickly to any scenes of violence”.
News – Clashes as police shut down Covid rules protest