Kian Delos Santos was shot by police who said he was involved in the drugs trade and had resisted arrest.
But surveillance footage appears to show the 17-year-old being dragged away by plainclothes officers.
Evidence suggests he was kneeling, faced down, when he was killed.
Hundreds of mourners attended his funeral in the capital, Manila.
Some held placards calling for an end to President Duterte's violent campaign.
The drive has been supported by many who are fed up with drug-related crime in the Philippines.
Nuns, priests and hundreds of children chanting "justice for Kian, justice for all" joined the cortege from a church to the cemetery where the boy was buried, Reuters news agency reports.
His father, Saldy, had spoken briefly during the Mass to insist on his son's innocence and vent his anger at the police.
"Don't they have a heart?" he asked, his voice cracking with emotion. "I'm not sure they do. There's a lot of churches, they should go there."
Father Robert Reyes was one of several Catholic priests who celebrated the Mass.
"Kian is the name and face of the truth," he was quoted as saying by AFP news agency. "We must not allow the truth to die with Kian's murder".
The boy's parents and lawyers filed a murder complaint against three drug squad police officers on Friday.
Human rights groups have accused Philippine police of planning extrajudicial killings and in some cases profiting from them.
Police have maintained that the suspects are killed when they offer armed resistance to police, a claim that has been highly disputed.
Mr Duterte suspended the campaign in January promising to "clean up" the police, and re-organise the anti-drug units. The campaign resumed in March.
The funeral has taken place in the Philippines of a teenager whose death sparked anger at President Rodrigo Duterte's anti-drugs campaign, which has led to thousands being killed.