The claims were made by a witness who was testifying Thursday before a Philippines Senate committee set up to probe alleged extrajudicial killings in the three months since Duterte became president.
The man, who identified himself as Edgar Matobato, testified that he was part of the 300-member "Davao Death Squad" (DDS), which he alleges was run on the orders of Duterte.
Matobato testified the DDS killed alleged drug dealers and criminals in the southern city of Davao, on the order of Duterte when he was mayor, between 1988 and 2013. More than 1,000 people were killed in Davao City alone, he claimed.
Matobato also accused Duterte of killing a member of the Department of Justice with an Uzi submachine gun while serving as mayor.
Duterte himself has not responded to the specific claims that he ran the DDS or killed a government official, but in the past has suggested that he did pull the trigger on suspects
in a kidnapping case.
President's office denies claims
During a regularly scheduled press conference Thursday, Duterte's communications secretary denied the claims.
When asked by a reporter whether he thought Duterte was capable of giving such directive, Martin Andanar said: "The Commission on Human Rights already conducted an investigation years ago, when the President was still a Mayor, and charges were not filed, they did not see any direct evidence."
Last year, Duterte addressed claims he was part of a death squad during a regular live weekly TV show broadcast in the Philippines.
"Me? They are saying that I'm part of a death squad? True, that's true
," he said in a mix of English and Visayan, a language spoken in southern Philippines, before threatening to kill thousands more criminals and dump them into Manila Bay if he was elected president of the Philippines.
He later retracted that statement, telling reporters there were "no Davao death squads," but the allegations remain and numerous local and international human rights groups have repeatedly criticized his record.
Matobato testified the death squad started out as a "liquidation squad" called "Lambada Boys," which he said was formed by Duterte.
"Our work was to kill criminals like drug pushers, rapists, snatchers. Those were the people we killed every day," Matobato said.
He described in gruesome detail their killing methods. He said they mutilated the bodies of their victims, cutting them up and dumping them on the side of the road, wrapping them in masking tape sometimes to avoid identification, and even feeding one body to a crocodile.
Matobato said the group grew in 1993 and evolved into the DDS. Its members consisted of former rebels and police.
Human Rights Watch said in a news release that it believes an independent investigation should be launched to probe whether Duterte had a role in the alleged extrajuidicial killings.
"President Duterte can't be expected to investigate himself, so it is crucial that the United Nations is called in to lead such an effort," said Brad Adams, the Asia director at Human Rights Watch.
Suspects 'buried in a quarry'
In his testimony, Matobato went into detail about several cases, including an alleged order by Duterte to "massacre the mosques of Muslims" after the Davao City Cathedral was bombed in 1993.
"A few days later, he ordered that we arrest and kill Muslim suspects, so we were staking out the Muslims," Matobato testified. He added the squad kidnapped and killed the suspects and buried them in a quarry.
When the Philippines Commission of Human Rights launched an investigation into the Davao killings in 2009, Duterte allegedly ordered the DDS to kill the Commission's Chairman Leila de Lima, according to Matobato. But the killing was not carried out.
Matobato also brought up other cases in his testimony, including one in 2010 when he alleged Duterte ordered the killing of his own sister's boyfriend.
Matobato accused Duterte of ordering the DDS to kill a journalist who was critical of him.
He also accused Duterte of killing a member of the Department of Justice with an Uzi submachine gun while serving as the mayor of Davao. "It was Mayor Duterte who killed him. He finished two Uzi magazines," Matobato said at the inquiry.
President's son implicated
And, in his testimony, he implicated Duterte's son Paolo, who is now Vice Mayor of Davao. He told the committee Paolo Duerte also ordered the DDS to kill people, and that Paolo was a drug user.
One of the people Paolo Duterte ordered killed was billionaire Richard King in 2014, with whom he was fighting with over a woman, Matobato said.
"People are like chickens in Davao," Matobato said.
Paolo Duterte posted a response on Facebook saying "What de Lima and this certain Matobato say in public are bare allegations in the absence of proof. They are mere hearsay. I will not dignify with an answer the accusations of a madman."
Witness says he was tortured
Matobao told the committee he quit the death squad in 2013 and was tortured and threatened to keep quiet about the killings.
He said he surrendered to the Philippines Commission of Human Rights and the Department of Justice in 2014 and was in witness protection up until earlier this year.
He left witness protection before Duterte took the presidency because he feared for his life, he said.
Duterte's war on drugs
Duterte has come under increasing international criticism for his war on drugs, which as of late August had claimed more than 1,900 lives.
Testifying before the Senate committee on August 23, Philippines National Police chief Ronald dela Rosa said that more 700 drug traffickers and users had been killed in police operations since July 1.
He said that the police "follow the rule of law" and that there was no shoot-to-kill order despite the growing toll of bodies piling up in the wake of Duterte's crackdown.
Duterte came into office with huge public support after he vowed to clean up the country of drugs and corruption.