A human rights watchdog has accused police in the Philippines of falsifying evidence to justify unlawful killings in the government's bloody war on drugs and pointed the finger at President Rodrigo Duterte as being ultimately responsible.

Human Rights Watch said on Thursday in a report that Duterte and other senior officials instigated and incited the killings of drug suspects in a campaign that could amount to crimes against humanity.

Police have repeatedly carried out extrajudicial killings of drug suspects, then falsely claimed self-defence, and planted guns, spent bullets or drugs on the bodies.

"Our investigations into the Philippine drug war found that police routinely kill drug suspects in cold blood and then cover up their crime by planting drugs and guns at the scene," said Peter Bouckaert, emergencies director at Human Rights Watch and author of the report.

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"President Duterte's role in these killings makes him ultimately responsible for the deaths of thousands."

The report said masked gunmen taking part in killings appeared to be working closely with the police, casting doubt on government claims that vigilantes or rival gangs are behind the majority of the killings.

It said that in several instances it investigated, suspects in police custody were later found dead and classified by police as "found bodies" or "deaths under investigation".

The United Nations should create an independent investigation to determine responsibility and ensure accountability, the report said.

Presidential spokesman Ernesto Abella said none of the accusations have been proven in court. Until that happens, "such claims are mere hearsay", he said.

National police spokesman Dionardo Carlos said Human Rights Watch should share its information with the police so any perpetrators can be charged in court.

Carlos said police data showed 2,500 people had been killed in police operations, while another 4,000-plus deaths were still being investigated, of which 680 were drug-related. Murder charges involving 1,330 victims have been filed with prosecutors or courts, but the details were not known.

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The Human Rights Watch report draws heavily on interviews in metropolitan Manila with 28 family members of victims, witnesses to police killings, journalists and human rights activists. It also references initial police reports of killings, which Human Rights Watch said its field research consistently contradicted.

Duterte barred the 170,000-strong national police from his anti-drug crackdown a few weeks ago after two anti-narcotics officers were implicated in the killing of a South Korean businessman in an extortion scandal that allegedly used the crackdown as a cover.

He announced on Tuesday that selected policemen will return to the anti-drug campaign, but that the main anti-narcotics agency will continue to supervise operations.