Philippine leader Rodrigo Duterte has been urged to end his war on drugs amid widespread anger at police over a schoolboy's brutal killing.

Allegations of a cover-up in the death of Kian Loyd delos Santos has caused rare outrage among the public in the Philippines, which largely supports Mr Duterte's campaign, which has seen more than 90 people killed in three nights of intensified police operations last week.

The 17-year-old student was killed in a rundown area of Manila and according to a forensic expert who conducted an autopsy, Mr Delos Santos was shot in the back of the head and ears while on the floor, suggesting there was no gunfight, contrary to an official police report.

The victim's family reject police allegations he was a drug courier.

Rodrigo Duterte says he 'doesn't give a s*** about human rights' as 3,500 killed in war on drugs

Mr Duterte has resolutely defended police on the front lines of his war on drugs, but he said the three officers involved in the teenager's killing should be punished if found to have broken the law.

The President said he had seen the CCTV footage acquired by media which showed plain clothes police dragging Mr Delos Santos to a location where he was later found dead.

CCTV footage appearing to show Kian Loyd delos Santos being dragged by plain-clothed police past a basketball court in Caloocan City Barangay, Philippines (Reuters)

Opposition Senator Leila de Lima, a detained critic of Mr Duterte, challenged the President to order the police to stop killing.

"I dare you, Mr President, to issue a clear and categorical order to the entire police force to stop the killings now," De Lima said in a handwritten note from a detention facility, where she is being held on charges of involvement in drugs trade inside jails, which she denies.

"Just say it. Do it now, please."

The most controversial quotes from Rodrigo Duterte Show all 9 1 /9 The most controversial quotes from Rodrigo Duterte The most controversial quotes from Rodrigo Duterte On killing drug addicts “These sons of whores are destroying our children. I warn you, don’t go into that, even if you’re a policeman, because I will really kill you. If you know of any addicts, go ahead and kill them yourself as getting their parents to do it would be too painful” The most controversial quotes from Rodrigo Duterte Message to China “I will go there on my own with a Jet Ski, bringing along with me a [Phillipino] flag and a pole, and once I disembark, I will plant the flag on the runway and tell the Chinese authorities, ‘Kill me’ ” AP The most controversial quotes from Rodrigo Duterte Christmas message to law-breakers “If you do not want to stop, and just continue committing crimes, then this would be your last Merry Christmas” AP The most controversial quotes from Rodrigo Duterte On sex life “I was separated from my wife. I’m not impotent. What am I supposed to do? Let this hang forever? When I take Viagra, it stands up” AFP/Getty Images The most controversial quotes from Rodrigo Duterte On the drugs trade “None of my children are into illegal drugs. But my order is, even if it is a member of my family, ‘kill him'" AP The most controversial quotes from Rodrigo Duterte Insulting the Pope “We were affected by the traffic. It took us five hours. I asked why, they said it was closed. I asked who is coming. They answered, the pope. I wanted to call him: ‘Pope, son of a wh**e, go home. Do not visit us again’” AFP/Getty Images The most controversial quotes from Rodrigo Duterte Joke about rape “I saw her face and I thought, 'What a pity... they raped her, they all lined up. I was mad she was raped but she was so beautiful. I thought, the mayor should have been first” AFP/Getty The most controversial quotes from Rodrigo Duterte Insulting Barack Obama "Mr Obama should be respectful and refrain from throwing questions at me about the killings, or son of a bitch, I will swear at you in that forum" REUTERS The most controversial quotes from Rodrigo Duterte On Abu Sayyaf Islamic militants "If I have to face them, you know I can eat humans. I will really open up your body. Just give me vinegar and salt, and I will eat you. If you annoy me to the fullest... I will eat you alive. Raw" EPA

Another senator, Risa Hontiveros, told the house Mr Duterte had blood on his hands and "reveled in the deaths of drug addicts", inspiring a culture of impunity and killing.

Filipinos tired of crime and drugs and supportive of the president had woken up to what was happening, she said.

"You had no choice but to confront his death because his narrative was compelling," she said of Mr Delos Santos.

"You felt stirred into action because you could no longer ignore the growing outrage ... there were thousands of deaths before him and that you allowed it to happen.

Social media users, politicians of all sides and Catholic bishops have called for an impartial investigation into the surge in killings by police, which stopped when news of the teenager's death surfaced.

The Senate will on hold an inquiry into last week's bloodshed later this week.

Protesters wearing masks depicting the victims of extra judicial killings taking part in a demonstration against the killings of suspected drug users allegedly by police during anti-drugs raids in Manila (TED ALJIBE/AFP/Getty Images)

Since Mr Duterte took office, more than 12,500 people, many small-time drug users and dealers, have been killed.

Police said around 3,500 of those were killed in gunfights with drug suspects who had resisted arrest and were shot by officers in self defence.

But human rights monitors believe many of the remaining two thirds were killed by assassins operating with police backing or by police disguised as vigilantes - a charge the police deny.