Diplomats from all continents condemned the reported surge of deaths during so-called anti-drug operations, which have claimed thousands of lives since Duterte took office last year.
The Philippines was facing its regular review at the Geneva-based UN human rights council, where each country's record is scrutinised every four years.
Monday's session was especially "critical because of the sheer magnitude of the human rights calamity" since Duterte's inauguration, Human Rights Watch said in a statement.
"There is no new wave of killings in the Philippines," Cayetano told the council.
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He said the government's enemies were using "a political tactic" of manipulating figures on extrajudicial killings to undermine the fight against a scourge that has poisoned Filipino society.
Cayetano also showed a video clip of Duterte vowing to put "drug lords ... Below (the) ground", an unusual move at the UN council where governments do not typically publicise death threats by their heads of state.
Delegations from Australia, Brazil, France, Germany and Ghana, among others, made identical calls.
China however offered support to the Filipino firebrand, declaring drugs "the public enemy of mankind."
A group of roughly 50 pro-Duterte supporters braved a light rain outside the UN earlier on Monday, hoisting placards proclaiming "Duterte is not a mass murderer."
Foreign governments and UN officials are free to criticise the president, protest organiser, Dexi Jimenez told AFP, but added that they need to understand "the war on drugs has gained (him) excellent ratings" in public opinion polls.
Since then, police have reported killing 2,692 people in anti-drug operations.
They say unspecified parties have murdered another 1,847 people in drug-related incidents, while 5,691 other violent deaths are under investigation.
In a major report on the drug war in February, Amnesty International accused police of shooting defenceless people, paying assassins to murder addicts and stealing from those they killed.
Duterte has previously boasted of taking part in killings.