The demonstrators were seen carrying a variety of signs, flags and placards as they crammed into the square, with some cheering, clapping and shouting “we will win”. No-one appeared to be wearing face coverings or sticking to social distancing measures.
Hours later, police said the event was being shut down because demonstrators were "putting people in danger of transmitting the virus". They warned that anyone who stays could be subject to enforcement action.
Officers were also seen removing sound equipment, while several protesters were led away in handcuffs. Another demonstrator was physically carried away from the scene by officers.
Piers Corbyn, the brother of former Labour leader Jeremy Corbyn, was among those at the event. Conspiracy theorist David Icke, who has made several false claims about coronavirus, was also in attendance.
In a statement, the Metropolitan Police 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.
“We are now asking those in Trafalgar Square to leave. Officers will be engaging with crowds and informing them of this development.
“By leaving now, you can keep yourself safe and avoid any enforcement action being taken by officers.
The protest comes 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.
The Metropolitan Police earlier said it had been engaging with organisers throughout the week to remind them of their legal obligations and explaining the events could be in breach of Covid-19 regulations.
While protests are exempt from the rule of six which is in force in England, organisers must submit a risk assessment and comply with social distancing.
Police said some organisers had done so but where this had not happened the Met will “increase their engagement and encourage attendees to disperse”.
They added that enforcement “remains a last resort but will be undertaken if required”.
Commander Ade Adelekan, who is leading the Met operation, said that, while there is “great frustration” at the regulations, a large midday protest could put the health of protesters and their contacts at risk.
He said: “I know there is great frustration to these regulations but they have been designed to keep everyone safe from what is a lethal 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 added: “Last weekend it was highly disappointing to see that a small minority of demonstrators targeted officers with violence. Some 15 officers were injured during this protest, with more than 32 arrests being made during the course of the day.
“I will not tolerate a repeat of this behaviour this weekend and officers will respond quickly to any scenes of violence.
Last week, thousands descended on central London to protest against mass coronavirus vaccinations.
The event, organised by opponents of lockdown measures, saw coronavirus sceptics and so-called "anti-vaxxers" holding banners and chanting “freedom” Some branded the Covid-19 pandemic a "scam", while others read: "Save our rights. No mandated vaccines." One protester held a banner calling for the Government’s Sage scientific advisers to be sacked, as another’s declared Covid-19 a “hoax”.
Scuffles broke out between some demonstrators and police, with officers moving in on protesters as they congregated near Nelson's column.
The protesters formed human blockades opposite the officers to stop them from making arrests.
Disputes broke out between the two sides next to the National Gallery, before officers were pushed back by the loud crowd, who began cheering and chanting.
Police removed sound equipment from Trafalgar Square and several protesters were led away in handcuffs.
Another demonstrator was physically carried away from the scene by officers.
By 3.45pm, tThe majority of anti-lockdown protesters were dispersed by police following brief clashes with officers dressed in riot gear.