The former chief police enforcer of Philippine president Rodrigo Duterte’s deadly war on drugs will be charged with corruption for allegedly protecting officers linked to the narcotics trade, the justice department has announced.

Oscar Albayalde resigned in October after serving as the Philippines’ police chief for more than a year, having presided over an anti-narcotics crackdown that left thousands of drug suspects dead.

The episode that led to his sudden fall from grace cast an unwelcome light on a drug war that is popular with Filipinos but has faced international criticism over allegations that police were summarily executing suspects.

The justice department said prosecutors found “probable cause” to charge Albayalde for not punishing officers accused of failing to account for 163kg of drugs and about US$517,000 seized from a drug raid.

A justice department statement said 13 other police officers would be charged with drug offences, corruption and taking bribes for their role in the operation in Pampanga province, north of Manila.

Albayalde has repeatedly denied having protected the officers or profiting from the seized drugs. In a statement he welcomed the case as an opportunity to clear his name: “Finally, I will have my day in court.”

The charge levelled against him carries a penalty of up to 10 years in prison.

The raid took place in November 2013 when Albayalde was Pampanga’s police chief.

Allegations of police graft and abuse are not rare in the Philippines. Duterte twice ordered police to stop the anti-narcotics campaign because of allegations of corruption and murder by officers.

In January police said they had killed 5,552 suspects in anti-drug operations since Duterte came to office in June 2016.

Human rights groups allege the real number is four times higher and say the killings are a crime against humanity. Prosecutors at the international criminal court have launched a preliminary probe of the campaign and the United Nations’ top rights body voted in favour of an in-depth review.

Although the drug war is overwhelmingly backed by Filipinos, critics say it targets the poor and leaves the rich and powerful untouched while reinforcing a culture of impunity.