During a Senate hearing, Edgar Matobato revealed he and others killed about 1,000 people over a 25-year period.
Edgar Matobato, 57, gave gruesome details of gangland-style hits, including feeding one victim to a crocodile.
Rodrigo Duterte’s spokesman rejected the allegations, saying investigations into his time as mayor had gone nowhere.
Edgar Matobato said he was a member of the Davao Death Squad, a notorious vigilante group allegedly responsible for hundreds of killings.
He said: “Our job was to kill criminals like drug pushers, rapists, snatchers.”
Edgar Matobato also claimed that Rodrigo Duterte’s opponents were targeted too, including four bodyguards of a local rival for mayor, Prospero Nograles.
Victims would be shot or strangled, he said, with some disemboweled and dumped into the sea so fish could eat them.
He told the Senate panel he went from a witness protection program into hiding when Rodrigo Duterte became president, fearing for his life.
Edgar Matobato also alleged Rodrigo Duterte ordered the bombing of a mosque in retaliation for an attack on Davao Cathedral in 1993.
On this claim Rodrigo Duterte’s spokesman, Martin Andanar, said: “I don’t think he is capable of giving those orders.”
Martin Andanar said the country’s Commission on Human Rights had failed to even prove the existence of the Davao Death Squad.
Prospero Nograles’ son Karlo, a Davao city representative, denied Eduardo Matobato’s account relating to his father’s bodyguards.
“I don’t know what this guy is talking about.
“I can only suspect that this guy is being manipulated by some people to only serve their own selfish interests,” Karlo Nograles wrote on Facebook.
The woman leading the Senate inquiry into extra-judicial killings, Leila de Lima, is a strong critic of Rodrigo Duterte and has been accused by him of having links to the illegal drug trade, something she denies.
Rodrigo Duterte became mayor of Davao in 1988, and his tough stance saw crime rates plummet, an approach he has vowed to replicate at national level.
Since his election this year more than 3,000 drug users and dealers have been killed amid international alarm over human rights violations.
Rodrigo Duterte has dismissed concerns over his drugs policies, calling UN Secretary General Ban Ki-moon “a fool” and insulting President Barack Obama as, something he later said he regretted.
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