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A self-confessed former death squad member who accused Philippine President Rodrigo Duterte of killing a government agent with an Uzi submachine gun has been denied official protection.

Edgar Matobato told a Senate hearing Mr Duterte had killed the public official while serving as mayor of Davao.

He was addressing an inquiry into extra-judicial killings.

He said he had gone from a witness protection programme into hiding because he feared for his life.

But he was told by the leader of Senate, Aquilino Pimentel, that his life was no longer in danger.

"I have denied the request for protective custody of the witness Matobato because there is no Senate rule to justify it," said Mr Pimentel.

Mr Matobato alleged the president had ordered the executions of hundreds of others.

His allegations were labelled "lies and fabrications" at the hearing while presidential spokesman Martin Andanar said investigations into the president's time as mayor had gone nowhere.

Mr Matobato said that as a member of the Davao Death Squad, a notorious vigilante group, his job had been to "kill criminals".

But he added that Mr Duterte's opponents had been targeted too, including four bodyguards of a local rival for mayor, Prospero Nograles.

He alleged that in 1993, the vigilante group had injured a justice department agent after a confrontation at a road block.

"Mayor Duterte was the one who finished him off," he said. "Jamisola [the justice department official] was still alive when he [Duterte] arrived. He emptied two Uzi magazines on him."