The teenager was among 96 people killed in the Manila area in what the police called a “one-time, big-time” crackdown on drug dealers and addicts in the capital and in several sprawling suburbs.
His death has rankled the government and forced Mr. Duterte to acknowledge publicly that there may have been lapses. On Saturday, the president’s spokesman, Ernesto Abella, said the government would not tolerate “wrongdoings or illegal acts” from any law enforcement officer.
That statement was a reversal from Mr. Duterte’s words last week, when he appeared to encourage the police to kill more drug suspects after praising them for a bloody anti-narcotics operation that has left nearly 100 people dead — the bloodiest siege so far since he began the campaign last year.
Mr. delos Santos’s death has raised serious questions about how the police conduct raids. Mr. Abella said that the government’s public prosecutor had filed criminal complaints of murder against the officers involved at the Justice Department — underscoring the “resolve” of the government, he added.
“Let us allow the legal process to run its course, and trust the justice system under the Duterte presidency,” Mr. Abella said.
The complaint followed a Senate inquiry on Thursday during which forensics investigators and the public attorney’s office testified that Mr. delos Santos had been shot at close range while kneeling.
That account contradicted the police’s narrative that he had been shot because he had fought with the officers. Pictures provided by investigators showed the dead teenager with a gun in his left hand, even though the boy was right-handed.
A closed-circuit television camera showed the police officers leading the boy away minutes before he was found lifeless in a nearby cul-de-sac with at least two gunshot wounds to the head and torso. Three witnesses, two of them minors, came forward to testify against the police.
“My son was begging them,” the elder Mr. delos Santos said at the march. “He said he wanted to go home because his father was looking for him. To the policemen who killed an innocent person, go to church. It’s not too late to ask for forgiveness.”
The politically influential Roman Catholic Church, which counts 80 percent of Filipinos as members, has used the death of the teenager to call on Mr. Duterte to stop what it called his ill-conceived war on drugs. On Saturday, one of its most outspoken priests, the Rev. Robert Reyes, led the funeral march and attacked Mr. Duterte’s campaign against crime, which he said was “clearly, a war on the poor.”
“I think if you look around, the majority of those who joined the march are from the ranks of the poor,” he said. “All were shouting, ‘Justice for Kian.’ People may be wondering, ‘Is this boy the new Ninoy?’ ”
He was referring to Benigno S. Aquino Jr., known as Ninoy, who staunchly opposed the dictator Ferdinand E. Marcos. Mr. Aquino was gunned down in 1983 on the tarmac of the Manila airport upon returning from exile in the United States. Mr. Marcos was widely blamed for the assassination.
His death united the opposition, and the effort grew into a “people power” revolution that toppled Mr. Marcos three years later. His widow later became president, and his son and namesake preceded Mr. Duterte in the position.
Whether Mr. delos Santos’s death will translate into a united front against Mr. Duterte is unclear.
“The call for justice has begun,” said Edwin Lacierda, a political strategist and former spokesman for the younger Mr. Aquino. “The Senate hearings and rallies have seen to that. That call for change has likewise begun, both from the people and those within the government.”
“Where it leads, we do not know,” he added. “But certainly, the people can no longer tolerate the binary attitude of condemning the killings but not calling to account” Mr. Duterte.
For the time being, he said, the boy’s death had forced the public “to face and confront reality, no longer with timidity.”
On Saturday, supporters of Mr. Duterte joined the crowd at the funeral march and cried with the boy’s father. Some, including Michael Alberto Darang, a 20-year-old college student, said he had voted for Mr. Duterte. He displayed a wristband bearing the president’s name.
“I used to believe in Duterte’s promise to end crime,” he said, “and in fact, I think that is partly true. But I never wanted deaths for the innocent. Stop these killings. Instead, arrest drug lords and others.”
He said it was clear that Mr. delos Santos had been a victim “of the police wanting to impress Duterte.”
“He promised us a better life,” Mr. Darang said of Mr. Duterte. “Death for the innocent is not the change we want.”