The 79-year-old Duterte didn't show up at the court in The Hague as expected on Friday, but appeared on a video screen from the detention centre where he is being held, about one-and-a-half kilometres away.
His lawyer, Salvador Medialdea, used the hearing to slam his arrest in Manila as a "pure and simple kidnapping."
He said Duterte "was denied all access to the legal recourse in the country of his citizenship, and this all in the nature of political score settling."
Presiding Judge Iulia Antoanella Motoc set a pretrial hearing date of September 23 to establish if prosecution evidence is strong enough to merit sending the case to trial. If a trial does go ahead, it could take years, and if Duterte is convicted, he faces a maximum sentence of life imprisonment.
The judge said that Duterte had been allowed to participate in his first ICC hearing by videoconference because he had just come off a long flight.
Duterte, wearing a jacket and tie, listened to the hearing through headphones, often with his eyes closed. He spoke in English to confirm his name, and his date and place of birth. He was not required to enter a plea. The hearing, which started about a half-hour late, lasted around 30 minutes.
Medialdea said that Duterte had been under observation at a hospital because of health issues.
The judge, addressing Duterte, said: "The court doctor was of the opinion that you were fully mentally aware and fit."
Estimates of the death toll during Duterte's presidential term vary, from the more than 6000 that the national police have reported and up to 30,000, according to numbers from human rights groups.
Duterte's daughter greets supporters outside court
His daughter, Philippine Vice President Sara Duterte, met with supporters outside the court before Friday's hearing and then visited him in the court's detention centre afterwards. Duterte is a political rival of the current president.
Duterte was arrested on Tuesday amid chaotic scenes in the Philippine capital after returning from a visit to Hong Kong. He was swiftly put on a chartered jet and flown to the Netherlands. After a series of medical checks on arrival, he was taken to the court's detention centre.
Duterte's supporters outside the court chanted ''Send him back! Send him back!" as they waited for his arrival.
Meanwhile, activists marched in the Philippine capital region, demanding justice for the thousands of suspects killed in Duterte's brutal crackdowns. Other groups set up large screens to allow families of suspects killed in the crackdowns to watch the ICC proceedings.
Prosecutors accuse Duterte of involvement as an "indirect co-perpetrator" in multiple murders, amounting to a crime against humanity for allegedly overseeing killings from November 2011 until March 2019, first while he was mayor of the southern city of Davao and later as president of the Philippines.
According to the prosecution request for his arrest, Duterte, as Davao mayor, issued orders to police and other "hitmen" who formed so-called Davao Death Squads, or DDS.
He told them "that their mission was to kill criminals, including drug dealers, and provided clearance for specific DDS killings," prosecutors allege, adding that he recruited, paid and rewarded the killers and "provided them with the necessary weapons and resources, and promised to shield them from prosecution."
Human rights groups and victims' families have hailed Duterte's arrest as a historic triumph against state impunity, while the former president's supporters have slammed what they call the government's surrender of a political rival to a court whose jurisdiction they dispute.
