Police Chief Ronald dela Rosa said on Monday that anti-drug units would be dissolved.
It comes after the murder of a South Korean businessman inside police headquarters. He had been kidnapped and killed by anti-drug police.
More than 7,000 people have been killed since the crackdown on drugs began.
Speaking on Monday, Mr Dela Rosa said Mr Duterte “told us to clean the organisation first”.
“We will cleanse our ranks… then maybe after that, we can resume our war on drugs.” “To all the rogue cops, beware! We no longer have a war on drugs,” Dela Rosa said.