Police Chief Ronald Dela Rosa said on Monday that anti-drug units would be dissolved.
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.”
The decision follows the recent murder of a South Korean businessman inside police headquarters who was kidnapped and killed by anti-drugs police.
Since the commencement of the crackdown on drugs, more than 7,000 people have been killed.
Many human rights groups have criticized President Rodrigo Duterte’s hardline stance against drugs but he enjoys the support of Filipinos.
Mr Duterte has made tackling drug use in the Philippines a central part of his presidency.
Durterte had promised to end war on drugs by Dec. 2016 but extended it to March 2017.
But recently at a press briefing, he said he was extending it to the last day of his tenure.
He said he had underestimated the depth of the drug problem.