Bangkok: The top law office in the Philippines has claimed the execution of a high school student that sparked a public outcry across the country was an "isolated case" and "collateral damage" was inevitable in President Rodrigo Duterte's war on drugs.

Justice Secretary Vitaliano Aguirre made the comments at a Senate inquiry which heard forensic evidence that 17-year-old Kian Loyd delos Santos was slumped on the ground when three bullets were fired into his head in Caloocan City, in Manila last week.

Police had claimed the killing was done in self-defence.

Human rights activists say the inquiry has exposed the abysmal failings of authorities to protect children from the deadly consequences of the crackdown that has left more than 12,000 Filipinos dead in 14 months.

According to the country's Children's Legal Rights and Development Centre at least 31 children, some as young as three, have been killed in police operations or vigilante-style killings  since Mr Duterte took office in June last year.

"Senator Aguirre's comments are not only callous and cynical, they are simply untrue," said James Gomez, Amnesty International's Director of Southeast Asia and the Pacific.

"There is no question that many children have paid the ultimate price for the police's shoot-to-kill approach and many more will unless the war on drugs is ended," he said.

Mr Gomez said those suspected of Kian's execution must be brought to justice.

"But investigation into one death is not enough, there must be the same level of accountability for all police killings," he said.

Three policemen have been suspended pending an investigation. On Friday, the Public Attorney's Office said it would seek murder charges against the three anti-narcotics officers.

Mr Duterte, who has said he would protect police carrying out his orders to kill drugs suspects or resist arrest, distanced himself from Mr Aguire's comments.

"That is the opinion of Senator Aguirre. But from the palace's point of view this is a serious matter and we have given it due attention," said Ernesto Abella, Mr Duterte's spokesman.

Kian's killing sparked widespread public outrage and condemnation from Catholic church leaders after CCTV footage and the testimony of witnesses showed the police lied about him resisting arrest.

Kian had no history of drug use or trafficking and worked from 5.30am to noon in his family's small shop before going to school every day.

Some of Mr Duterte's closest allies in the Senate broke ranks and voted to set up the inquiry.

A photo of Nick Warner, Australia's overseas spy chief, pumping a fist with Mr Duterte in Manila this week also prompted criticism from human rights activists, who said it could signal Australia's support for the crackdown.

Foreign Minister Julie Bishop said Mr Warner, the director-general of the Australian Secret Intelligence Service, was asked by Mr Duterte to pose for the cameras after a private meeting. 

Ms Bishop has said Australia's is "deeply concerned" about the killings.

The toll in the crackdown so far is the largest number of civilian deaths in south-east Asia since the 1970s Khmer Rouge genocide and the Vietnam War.

The United Nations has said the killings could amount to a crime against humanity.