The chief of police in the Philippines has stepped down after facing historical accusations in the Senate that he protected officers who had resold confiscated drugs and received some of the profits.

It was a rapid fall from grace for Oscar Albayalde, the head of the Philippine National Police (PNP), who rose to fame as the enforcer of Rodrigo Duterte’s war on drugs in Manila before Duterte was appointed president. Albayalde has denied the allegations.

Thousands of people have been killed as part of Duterte’s campaign against illegal drugs. Amnesty International called it a “large-scale murdering enterprise”.

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“After careful deliberation, I have come to the decision to relinquish my post as chief, PNP, effective today and go on a non-duty status. I have submitted my letter of intent to [interior secretary Eduardo Año] which he accepted and favourably endorsed to the president,” Albayalde said in an address to police on Monday morning. It comes weeks before his scheduled retirement on 8 November.

The shocking allegation stemmed from a 2013 anti-drug raid in Pampanga province in Central Luzon, when he was a provincial police chief. He allegedly sought to stop the dismissal of officers under him who were found to have taken and hidden more than 100kg of shabu, or methamphetamine, as a bribe from a drug suspect so he could escape. A fall guy was arrested instead.

Facebook Twitter Pinterest Philippine national police chief General Oscar Albayalde Photograph: Bullit Marquez/AP

A retired police general made the revelation accidentally during a Senate inquiry on another topic. Benjamin Magalong, the retired head of the criminal investigation and detection group, testified that Albayalde made a call to intervene in the investigation of the raid. Senators pursued the matter and another retired general, who investigated the controversial raid, came forward to allege Albayalde told him he “got a little” from the profits.

The Senate probe established irregularities in the controversial raid and found the reports the police filed were inconsistent. It also found the police were slow in punishing corrupt personnel. Magalong claimed the officers involved in the raid were given desirable posts under Albayalde.

Albayalde’s resignation comes after a weekend conversation with Año, whom Duterte ordered to investigate allegations against him.