Director General Oscar Albayalde, who was sworn in Thursday, will now lead the narcotics crackdown that has killed thousands since Duterte came to power just under two years ago.
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"How to sustain the drug war? In order to sustain it, we will not change anything," Albayalde told reporters at his first press conference as commander.
He took over from Ronaldo Dela Rosa, who retired with hero's honours this week after helping Duterte launch the bloody crackdown.
"Why would we stop a programme that is very effective?" Albayalde added, citing "very good momentum and gains" since the alleged police killing last year of a teenage boy wrongly accused of drug crimes that sparked street protests.
Police on Friday announced another 13 alleged drug suspects were killed in a sweep that also led to the arrest of 58 people.
Albayalde's comments came as the Philippines pushed back against a European Union Parliament resolution voted on Thursday that criticised the crackdown, the latest international condemnation of it.
The EU lawmakers called "on the government of the Philippines to put an immediate end to the extrajudicial killings in the pretext of a 'war on drugs'".
It also expressed "grave concern over credible reports to the effect that the Philippine police force is falsifying evidence to justify extrajudicial killings".
While police say the campaign has killed around 4,100 people, rights groups allege the true toll is triple that number and amounts to state-sponsored murder.
Duterte began the crackdown in July 2016 after pledging during the presidential election campaign to kill 100,000 criminals to rid society of the scourge of narcotics.
Philippine Foreign Secretary Alan Peter Cayetano on Thursday denounced the EU parliamentary resolution as "interference" in Manila's internal affairs, describing it as "biased" and "based on wrong information".
Duterte last month pulled his country from the International Criminal Court after The Hague-based body's chief prosecutor launched an initial examination into allegations lodged against the president over his drug war.
He also threatened to arrest the chief ICC prosecutor, Fatou Bensouda, if she tried to enter the Philippines to pursue her investigation.
On Sunday the Philippines deported EU politician Giacomo Filibeck, who has previously criticised Duterte's crackdown, and on Monday briefly detained an elderly Australian nun who has been critical of alleged human rights violations by Philippine soldiers.
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