The first charge cites 19 victims killed while Duterte was mayor of Davao City between 2013 and around 2016.
The second involves 14 who died in targeted killings between 2016 and 2017 when Duterte was president.
The third cited the killings of 43 people during so-called "clearance operations" between 2016 and 2018.
The redacted charges were made public on Monday after prosecutors submitted a 15-page charge sheet to the court on July 4.
Among other things, they allege Duterte instructed and authorised "violent acts including murder to be committed against alleged criminals, including alleged drug dealers and users".
Duterte, his lawyer and family did not immediately react to the detailed charges.
Even when he was president, he denied authorising extrajudicial killings although he openly threatened drug suspects with death and encouraged police to open fire if suspects violently resisted arrest and threatened law enforcers.
Duterte was arrested in March by Philippine authorities on a warrant issued by the ICC.
He is being held at an ICC facility in the Netherlands.
Supporters of Duterte criticised the administration of President Ferdinand Marcos Jr, Duterte's political rival, for arresting and surrendering the former leader to a court whose jurisdiction his supporters dispute.
A court hearing had been scheduled to begin on Tuesday but was postponed to give judges time to evaluate arguments from Duterte's lawyers that he is not fit to stand trial.
