Manila (AFP) - Rodrigo Duterte shot dead a justice department employee and ordered the murder of opponents, a former death squad member told parliament Thursday, in explosive allegations against the Philippine president.

The self-described assassin testified under oath that he and a group of policemen and ex-communist rebels killed about 1,000 people between 1988 and 2013 on Duterte's orders -- one of them an alleged kidnapper fed alive to a crocodile.

Others were garroted, burned, quartered and then buried at a quarry owned by a police officer who was a member of the death squad. Others were dumped at sea to be eaten by fish.

Edgar Matobato, 57, made the allegations before the Senate, which is investigating alleged extrajudicial killings in Duterte's anti-crime crackdown that police said has left 3,140 people dead in his first 72 days in office.

Justice Secretary Vitaliano Aguirre called the allegations "lies and fabrications", adding Matobato "is obviously not telling the truth".

Duterte aides said the government's Commission on Human Rights had already investigated the allegations but did not file charges while his son, Paolo Duterte, called the testimony "mere hearsay" of "a madman".

The then head of the Commission on Human Rights, Senator Leila de Lima, told the inquiry Matobato had surrendered to the investigatory body in 2009 and had until recently been in a witness protection scheme.

Matobato recounted a 1993 death squad mission that was unintentionally impeded by the vehicle of an agent of the justice department's National Bureau of Investigation that was blocking a road on the southern city of Davao.

The agent ran out of bullets and was wounded in a shootout before Rodrigo Duterte, the Davao mayor at the time, showed up armed with a submachine gun, Matobato said.

"Mayor Duterte was the one who finished him off.... He emptied two Uzi magazines on him."

- 'Like chickens' -

"I didn't kill anyone unless ordered by Charlie Mike," he said, telling the senate it was the death squad's coded reference to city mayor, referring to then-mayor Duterte.

Story continues

Matobato's testimony fleshed out in gruesome detail for the first time long-running allegations Duterte was behind the killings of more than a thousand petty criminals, including minors, in Davao, where he was mayor for most of the past two decades.

"Our job was to kill criminals, rapists, pushers, and snatchers. That's what we did. We killed people almost on a daily basis" between 1988 and 2013, said Matobato, adding they also killed Duterte family foes and an "international terrorist".

"The people of Davao were being slaughtered like chicken," he said, adding he lied to his wife about butchering chickens when she saw his blood-spattered shirts.

"I don't think he's capable of giving a directive like that," Duterte spokesman Martin Andanar said, adding that the government's human rights commission investigated the allegations but did not file charges.

Duterte, who took office more than two months ago, won May elections in a landslide on a promise to kill thousands of criminals.

He has rejected calls by the United States, the United Nations and rights groups to stop extra-judicial killings.

Matobato said he received orders to kill either directly from Duterte or from active-duty Davao police officers assigned to the mayor's office who were also part of the death squad.

- 'Disembowelled bodies' -

"The officers told us ordinary killings won't do. They are sadists," he said, describing how the victims were strangled.

"Then we'd remove their clothes, burn the bodies and chop them up," Matobato said, adding that he had personally killed "about 50" people.

Some victims were disembowelled and dropped at sea, while others were left on Davao streets with rusty handguns planted in their hands to simulate a gun battle, he added.

The boyfriend of Duterte's sister, along with Davao broadcaster and Duterte critic Jun Pala, four bodyguards of a local rival, and two enemies of Duterte's son Paolo, now Davao vice mayor, were also killed, Matobato added.

"I will not dignify with an answer the accusations of a madman," Paolo Duterte said, calling the allegations "mere hearsay".

President Duterte has denied ordering Pala's 2003 Davao ambush but has described him as an extortionist and a "rotten son of a bitch" who "deserved it". The UN and rights watchdogs roundly denounced his comments.

De Lima said the rights body later dug up several skeletons of unidentified people at the Davao quarry.

She said the hitman's testimony would be referred to the Philippine Ombudsman, although she acknowledged sitting presidents are immune from prosecution and could only be removed through impeachment.

Matobato said the death squad "tortured" him when he asked to leave the group in 2013, telling his bosses he was "too old" for it and wanted to look for a proper job.

He was admitted to the justice department's witness protection programme but left to go into hiding when Duterte won the presidency, Matobato added.

Asked why he left the death squad, he replied: "I am bothered by my conscience."