The incident occurred on Thursday night when police were called to a Manila suburb following an earlier shooting during an argument between residents.
But they mistakenly opened fire on a van that they thought was carrying the shooter but which in fact was taking a woman injured in the incident to hospital, said district police chief Senior Superintendent Moises Villaceran.
"Our police thought these were among the people that opened fire earlier," Villaceran told reporters.
Videos of the incident, aired on local television, show policemen with guns drawn, surrounding the van as gunshots ring out.
Initial reports showed that two people were killed while two others were wounded, a police aide of Villaceran told AFP Friday.
The deadly shooting comes as Duterte wages a brutal war on drug-related crime, openly urging police to kill suspects and vowing to protect them from legal liability in such incidents.
Government figures show that almost 4,000 "drug personalities" have been killed by government forces as part of Duterte's anti-drug campaign since he took office in mid-2016.
Human rights groups charge that thousands more have been killed by shadowy vigilantes.
(Except for the headline, this story has not been edited by NDTV staff and is published from a syndicated feed.)
Get Breaking news, live coverage, and Latest News from India and around the world on NDTV.com. Catch all the Live TV action on NDTV 24x7 and NDTV India. Like us on Facebook or follow us on Twitter and Instagram for latest news and live news updates.