Duterte issued his warning on Monday as the death toll from his controversial crackdown climbed above 4,800, or roughly an average of 30 deaths a day since it began five months ago.
"The human rights (defenders) say I kill. If I say: 'Okay, I'll stop'. They (drug users) will multiply," Duterte said.
"When harvest time comes, there will be more of them who will die. Then I will include you among them because you let them multiply," he added.
"This pronouncement is... Inciting hate towards anyone who expresses dissent on his war against drugs," it said in a statement.
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The National Alliance against Killings Philippines, a newly formed coalition of rights groups, said it took the threat very seriously and called on Duterte to revoke it.
"His comment -- that human rights is part of the drug problem and, as such, human rights advocates should be targeted too -- can be interpreted as a declaration of an open season on human rights defenders," it said.
"This (threat) is a continuation of his effort to create a culture of fear, a culture of violence. We will not let this come to pass," he told AFP.
Fajardo said the Catholic Church, which counts more than 70 percent of Filipinos as followers and has so far been subdued in its criticism of the drug war, was starting to find its voice on the issue.
"That is why he is more threatening. He cannot just frighten us. The priests and nuns will speak out," he said.
Since assuming office, he has called on police and even civilians to kill drug users.
Duterte also said he would be "happy to slaughter" three million drug addicts, and likened his campaign to Nazi leader Adolf Hitler's efforts to exterminate Jews in Europe.
The 71-year-old lawyer later apologised for his Hitler reference, but said he was "emphatic" about wanting to kill drug users.
Nevertheless, Duterte has also repeatedly insisted that nearly all of the people killed were either resisting arrest or murdered by fellow gangsters.
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