He was elected to office in 2016 on a campaign promise to get rid of the country's drug problem, openly ordering the police to kill drug suspects if their lives are in danger.
More than 6,000 people have been killed in over 200,000 anti-drug operations conducted since July 2016, the latest official data show. Human rights groups estimate the number of dead could be several times higher.
The ICC's Bensouda said the court "does not take a position on any government's internal policies" to combat drugs but that it was acting under its mandate to investigate war crimes and crimes against humanity.
"The available information indicates that members of the Philippine National Police, and others acting in concert with them, have unlawfully killed between several thousand and tens of thousands of civilians" during the period under investigation.
The court would also investigate allegations of torture and other "inhumane acts" dating back as far as 2011, it said.
'Drug watch lists'
Many suspects had been put on "drug watch lists" by local officials and then visited by police at their homes, which often ends in a deadly shooting that officers claim was self-defence.
The tough-talking president has repeatedly claimed the ICC has no jurisdiction over him and that he will not cooperate with what he has called an "illegal" probe.
He even threatened to arrest the former ICC prosecutor Fatou Bensouda.
Bensouda however said previous cases showed that "the court retains jurisdiction over crimes that are alleged to have occurred on the territory of that state during the period when it was a state party" to the ICC.
Duterte has previously told the tribunal that the country's justice system is working amid allegations that local courts cannot or are unwilling to prosecute suspects in the killings -- one of the criteria for the ICC to open a full investigation.
Duterte has said he is willing to go behind bars if proven guilty in the Philippine judicial system.
"If the court says that I should go to jail, I will go to jail. That's no problem. I did what I embarked to do," Duterte said in a televised speech in December 2020.