ZAMBOANGA CITY, the Philippines

A hitman turned key witness at a senate probe into extrajudicial killings has filed murder and kidnapping charges against the Philippines president, accusing him of genocide and crimes against humanity.

Edgar Matobato, a self-confessed member of the Davao Death Squad since 1998, filed his complaint-before the office of the ombudsman Friday morning.

Human rights groups claim the squad has killed at least 1,400 robbers, rapists, and other suspected criminals since the early 1990s in Davao city -- where President Rodrigo Duterte was previously mayor.

A report Friday from news website Rappler said that Matobato's charges also included criminal and administrative complaints against Duterte's son, Davao City Vice Mayor Paolo Duterte, national police chief Director Gen. Ronald dela Rosa and 25 members of the squad.

Duterte -- who has been accused of forming the squad -- has repeatedly denied involvement in vigilantism either as mayor of Davao or president -- critics say a bloody war on drugs which has seen 4,248 killings between his inauguration June 30 and early October invoked similar methods.

Matobato said he had filed Friday's complaint to seek "justice" for alleged victims of the squad, claiming it was responsible for over 1,000 murders from when he joined until September 2013.

He has previously said that the victims "were killed like chickens," and claimed that Paolo Duterte was a drug user who ordered the death of a hotel owner in 2014.

"Mayor Duterte is the leader of the DDS. The Lambada Boys' code name for him is 'Charlie Mike' or 'Harry/Hari'," Matobato said in his affidavit, referring to a group which was allegedly the precursor of the squad.

"Nearly all operations have to be cleared with Duterte," he claimed. “He ordered the killings. If the victim is known or big-time, Duterte would go to the Laud Quarry to make sure of the identity of the target and to watch the dismemberment of the corpse."

Matobato's lawyer told the senate that another witness will be presented to back up Matobato's allegations.

In a statement released Friday, Presidential Communications Assistant Secretary Ana Marie Banaag called Matobato's charges "nothing but harassment aimed at distracting the chief executive [Duterte] from performing his duty”. 

“It is noteworthy to mention that the ombudsman cannot discipline or remove impeachable officials, which include the president. He enjoys immunity while in office,” she underlined.

Banaag noted that the ombudsman had already terminated an earlier investigation into the death squad and alleged links to then Davao City Mayor Duterte.

On Wednesday, a joint committee report on state killings and death squad existence said 4,248 killings had taken place in the Philippines from July to the early part of October, yielding an average of 47 killings per day over the period.

In the 89-page report, it said there was no sufficient evidence to prove Duterte's administration sponsored summary killings in the Philippines, nor was there proof of so-called death squads.

The probe that led to the report was initiated by Leila de Lima, a human rights advocate, and staunch critic of Duterte who previously headed the justice committee until she was ousted from the post and replaced by senator Richard Gordon.

Critics have accused Gordon of being little but a Duterte "lackey".