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The resolution was put forward by Iceland at the Human Rights Council in Geneva Thursday and passed with 18 votes. Fifteen countries abstained, and 14 voted against it.
International human rights groups and UN bodies have previously expressed concerns about the Duterte administration's scorched earth-approach in its efforts to eradicate the methamphetamine trade.
The Philippines Secretary of Foreign Affairs, Teodoro L. Locsin Jr., said the UN Human Rights Council's decision Thursday "flies in the face of everything the Philippines has worked for when it founded the Human Rights Council." The council was formed in 2006 by a UN general assembly resolution.
"We will not accept a politically partisan and one-sided resolution, so detached from the truth on the ground. It comes straight from the mouth of the Queen in Alice in Wonderland, 'First the judgment, then the proof,'" Locsin said in a statement.
"Do not presume to threaten states with accountability for a tough approach to crushing crime," he also said.
Duterte's critics contend that his government is engaging in gross human rights abuses by using extrajudicial killings against drug dealers.
The Philippines National Police have said more than 6,600 have been killed during anti-drug operations, but independent monitors believe the numbers are much higher.
"Three years on, President Duterte's 'war on drugs' continues to be nothing but a large-scale murdering enterprise for which the poor continue to pay the highest price," Nicholas Bequelin, Amnesty International's regional director for East and Southeast Asia, said in a statement.
Duterte and his administration have long voiced opposition to international criticism to the drug war, claiming it is the government's sovereign right to protect the Philippines people from the scourge of addiction.
"You're investigating us? Fact finding? Sorry, do not f*** with me," Duterte said shortly after the ICC announcement last year.
"Who are you to interfere in the way I would run my country? You know very well that we are being swallowed by drugs."