Footage from the scene on Second Avenue at East 25th Street shows three NYPD policemen wrestling the protester to the ground before shoving her into the unmarked silver minivan.
A group of uniformed officers then arrives, some of whom are riding bicycles. They can be seen guarding the vehicle while the protester is detained.
Officers then push away other protesters attempting to intervene before the vehicle speeds off.
It is unclear as to what happened prior to the video recording. A demonstration had taken place at Abolition Park earlier in the day.
Local officials reacted furiously to the arrest. Alexandria Ocasio-Cortez, US representative for New York’s 14th congressional district, warned: “Our civil liberties are on the brink”.
“This is not a drill,” the Democrat politician wrote on Twitter. “There is no excuse for snatching women off the street and throwing them into unmarked vans.
“To not protect our rights is to give them away. It is our responsibility to resist authoritarianism.”
Jerry Nadler, rep for New York’s 10th congressional district, called for an “immediate explanation for this anonymous use of force.”
“This video — of a protester in New York City being thrown in an unmarked van — is terrifying and should be unacceptable to everyone who respects the constitutional rights this country was founded on,” he wrote on Twitter.
The NYPD later said in a statement that the woman was arrested for damaging five police cameras during separate criminal incidents in and around City Hall Park.
The force also claimed the arresting officers were assaulted with rocks and bottles. NYPD’s warrant squad uses “unmarked vehicles to effectively locate wanted suspects”, the statement added.
Demonstrations continue to sweep the US more than two months after the death of George Floyd in police custody.
Tensions have been flaring in some cities after the Trump administration deployed federal officers to police protests.
The use of unmarked vehicles to arrest protesters first came to attention in Portland, Oregon after a number of people were detained there earlier this month.