During its 41st session in Geneva, 18 of the 47 member states of the council voted in favour of the resolution filed by Iceland, which formally asked United Nations rights chief Michelle Bachelet to come up with a comprehensive report on the situation in the Philippines.
Eighteen countries voted in favor of the Iceland-endorsed resolution, 14 were against, and 15 abstained during voting held in Geneva Thursday.
The measure, presented by Iceland, cites allegations of thousands of killings since President Rodrigo Duterte launched a campaign against illegal drugs in mid-2016.
Philippine Foreign Secretary Teodoro Locsin has rejected the resolution and warned "there will be consequences" for those countries who backed it. The country's ambassador in Geneva, Evan Garcia, said it "does not represent a triumph of human rights, but a travesty of them".
The resolution calls on national authorities, including the Filipino government, to take all necessary measures to prevent extrajudicial killings, arbitrary arrests and enforced disappearances.
While the resolution did not establish a full commission of enquiry, as many activists had hoped it would, the green light for Bachelet to begin investigations is the council's strongest condemnation of Duterte's actions yet and could have severe consequences. But nongovernment groups claim a much higher death toll, including many suspects killed by motorcycle-riding gunmen who human rights groups suspect were deployed by police.
Locsin added that in light of this resolution, which was backed by several countries the Philippines considers allies including the United Kingdom and Australia, the foreign policy of the Philippines had shifted from "friend to all, enemy to none" to "friend to friends, enemy to enemies, and a worse enemy to false friends".
About 6,600 people, majority accused of petty drug crimes, have been killed in the crackdown that Duterte launched as his centerpiece project when he took office in mid-2016.
Sotto had earlier branded the resolution as "biased" and advised the Philippine government to disregard it.
"We don't probably need anybody or even especially global human rights committee para mag-conduct pa (to conduct it)". Activists say thousands are being killed as police terrorise poor communities, using cursory drug 'watch lists to identify suspected users or dealers, and executing many of them under the guise of sting operations.
Last week, a three-year-old girl became one of the crackdown's youngest victims after she was shot dead in a drugs raid. Police say her father Renato had used her as a human shield.
This is a significant step towards justice.
"The resolution is grotesquely one-sided, outrageously narrow, and maliciously partisan", Panelo said in a lengthy statement issued overnight. There will be consequences: far-reaching ones. "As long as they are job-related, they're on me", he said.
In March, the Philippines withdrew from the International Criminal Court, which is examining Duterte's anti-drug campaign.