The Philippines' top policeman, who leads the nation's deadly drugs crackdown, quit on Monday as he faces allegations of protecting officers accused of selling a huge haul of seized narcotics.

Though the scandal dates from before Oscar Albayalde's time as national police chief, it has raised fresh criticism of President Rodrigo Duterte's signature campaign, which is key to his massive popularity among Filipinos.

As part of the president's internationally condemned initiative, police have killed thousands of alleged dealers and users since mid-2016, but critics say the wealthy and powerful have been largely untouched.

Albayalde's resignation comes days after two former police officials implicated him in a 2013 raid in which officers in a province near Manila allegedly seized and then sold parts of a large methamphetamine haul.

One former official alleged Albayalde protected the officers from discipline, while the other claimed he received money from the drug sale.

Albayalde, then the province commander, has vehemently denied any wrongdoing.

He was due to retire in November after serving as national police chief since April 2018.

"I thank President Rodrigo Roa Duterte for his trust and confidence," Albayalde said in a message announcing his departure, which is effective immediately.

Though the issue has been bubbling for weeks in Senate hearings, Duterte has remained largely silent on the matter.

He had pledged to root out deep-seated corruption in the Philippines' police but has repeatedly expressed frustration and anger with the extent of the problem.

Neri Colmenares, a lawyer for families pushing for an International Criminal Court prosecution of the drug war, branded the allegations against Albayalde a "major embarrassment".

"Even the presiding officers of the PNP (national police) are involved in drugs themselves," he said. It "shows what we've been saying all along, this is targeted against the poor."