Interior Secretary Juanito Victor Remulla Jr said Ronald dela Rosa, who is now a senator, will be summoned on Monday.
The thousands of killings of mostly impoverished drug suspects took place when Duterte was mayor of the southern city of Davao and after he became president in 2016.
The killings during police raids alarmed human rights groups and Western governments led by the United States.
Duterte, 81, was arrested in March 2025 and taken to the Netherlands, where he is facing trial at the International Criminal Court for alleged crimes against humanity.
Dela Rosa, a former Davao city police chief who was appointed by Duterte to lead the national police force, has been summoned amid speculation that he faced imminent arrest on the order of the ICC.
He has not appeared at the Senate since November 2025 after reports surfaced that he would be arrested.
Duterte, dela Rosa and other police officials have denied authorising the killings of drug suspects, who, they said, were shot dead after allegedly threatening law enforcers. Duterte openly and repeatedly threatened drug suspects with death while in office.
A 2024 congressional investigation recommended criminal charges to be filed against Duterte and key police officials involved in the crackdowns.
Dela Rosa "has never been personally investigated," Remulla said.
"All officers involved must be held accountable and, just to be clear, he was the tip of the spear in the extrajudicial killings drive, so we will start with him and investigate down further."
Remulla said the investigation into dela Rosa will be "the start of the process to find accountability to everything that happened in those dark years where extrajudicial killings became a state policy".
