The outspoken president hit out at Brussels days after rejecting £216million aid package from the bloc.
Mr Duterte’s war on drugs has seen thousands killed in a major crackdown that has alarmed much of the international community.
In an interview with RT, he said: “My orders were very clear: Go out and hunt for them, the drug lords. Arrest them if possible, but if they confront you with violence that placed the lives of policemen or security forces in danger, kill them.
“Because in the past this was what really prevented policemen and the military from doing it. Why? Because they were so afraid of the human rights thing, which is a new phenomenon.
“Actually, in the guise of the human rights, countries like EU and America are interfering into the affairs of other nations. In the guise of human rights.”
Responding to criticism over his bloody campaign, Mr Duterte defended the killings of innocent civilians adding the US “is exempt” to condemnation over its own track record.
He said: “We are talking about human liability. So, it doesn’t say that, because they are Americans, they are exempt. And just because I am a small time government official, I am not exempt. So, where’s the fairness there? No? When they drop bombs, they kill so many villages, and there’s not even a whimper.
“America invaded Iraq. What was the excuse? That there were weapons of mass destruction. And yet when they invaded Iraq, so many people were killed. So where is justice now?”
Earlier this year Mr Duterte hailed US president Donald Trump as a “realist” and “deep thinker” after the new White House administration invited him to Washington.
But tensions have frayed with Mr Duterte refused the invitation and turned his back on the West in the hope of building up alliances with Russia and China.
It comes as the Philippines said its relationship with the EU would be “a rocky, rollercoaster ride” after Mr Duterte rejected a £216million foreign aid package.
Foreign Secretary Alan Peter Cayetano told reporters the government would have accepted the aid had the EU not imposed conditions related to Mr Duterte’s war on drugs.
Mr Cayetano said: “We have good relations with the EU, but it’s going to be a rocky period, or a rollercoaster ride,” Cayetano said, adding that he would meet the EU ambassador next week when he returns from an overseas trip.
“We will try to navigate this rollercoaster ride together.”