Delhi's Shaheen Bagh - heart of protests against CAA - was cleared after 101 days.
Cops reached the site of the protest at around 7 am on Tuesday
Shaheen Bagh had inspired many similar protests across the country.
Gatherings have been banned under Section 144 over COVID-19.
Nine people, including six women and three men, have been detained.
The protest site is set to be cleaned up with the help of civic body
Protests against CAA in Jaffrabad and Turkman Gate old Delhi were also removed.
This comes two days after Chief Minister Arvind Kejriwal announced a lockdown in the city
"Extraordinary times call for extraordinary measures," he had tweeted.
The national capital has reported over 30 coronavirus cases, including one death.
Public transport is closed, borders are sealed and shops closed allowing in only the essential items.
Across India, over 500 cases have been reported, including nine deaths.
Thirty states and union territories are under complete lockdown.
Delhi Police had urged the anti-CAA protesters to call off their agitation.
The protesters, who began their sit-in on December 15, did not agree to the request.
The sit-in would continue, they had said, with "necessary precautions".
The size of the gatherings was reduced after repeated requests by authorities.
Delhi police also cleared the protest site outside Jamia Millia Islamia on Tuesday
It has been ensured that no protests take place amid lockdown
JMI had temporarily suspended the protest on March 21 at Gate no. 7 in view of coronavirus.
Police also used drones to monitor the area.
The Shaheen Bagh protest had made international headlines over the last few months.