Television footage showed the van repeatedly running back and forth into and over protesters.
The van suddenly reversed and then sped forwards twice over a distance of some 20 yards, knocking down and scattering protesters. The activists ran for safety but several people were hit by the police vehicle.
Renato Reyes, of the activist group Bayan, told BBC there was "no justification" for the police violence. "Even as the president vowed an independent foreign policy, Philippine police forces still act as running dogs of the U.S.".
Police arrested 23 protesters who broke into a line of riot police and hurled red paint at officers and a USA government employee. After breaking through the police corridor, they wrote "US troops out now" and other slogans in red paint on the embassy's tall fence.
But the protesters also opposed the president's effort to lean toward China.
Photos and videos from the event appear to show police throwing tear gas at protesters, and, at one point, dousing them with a powerful spray of water from a fire truck hose.
Duterte is now at Beijing, seeking to deepen ties and economic relation with China and has announced that Philippine will separate with U.S. on its military and economic ties after decades of collaboration. "President Rodrigo Duterte has said that he, too, wants the USA troops out".
President Rodrigo Duterte on Saturday said he will personally look into the violent dispersal of militant protesters outside the United States embassy earlier this week.
"Congress must not allow such fascistic actions of the Philippine National Police to prosper under the new administration, particularly against the marginalized sector of our society like the national minorities", read the House resolution.
Twenty-five protestors and 30 police officers were injured in the incident and 21 protesters were briefly detained, said capital region chief of police, Oscar Albayalde.
Police have yet to confirm the number of protesters arrested.
He insisted that he does not want to see future violence between police and protesters.
A total of 23 protesters were arrested, said Chief Inspector Arsenio Riparip, one of the officers overseeing the incident. "They have to go in Mindanao, there are many whites there, they have to go", he said, adding that he was reorienting the country's foreign policy. I saw people get hurt. In response, Mr Duterte has insulted US President Barack Obama and the US ambassador to the Philippines.