Listing some of Manila's actions against UN envoys, including filing terrorism charges against one, rights chief Zeid Ra'ad Al Hussein said "it makes one believe that the president of the Philippines needs to submit himself to some sort of psychiatric evaluation".
Zeid and other UN rights officials have focused significant attention on Duterte's controversial drug war.
Police have killed more than 4,100 drug suspects since Duterte took office in 2016, but rights groups allege more than 8,000 others have been murdered in what they describe as crimes against humanity.The UN special rapporteur on extra-judicial killings, Agnes Callamard, has become a particular Duterte target over her criticism of his campaign to stamp out illegal drugs.
Earlier this month, Duterte vowed he would never cooperate with UN investigators looking into extrajudicial killings.
"When the human rights or whoever is that rapporteur arrives, my order to you is, do not answer ...
"You're investigating us, fact finding? Well sorry, do not fuck with me," the president said, referring to Callamard.
Speaking to reporters on Friday, Zeid said it was "absolutely disgraceful that the president of a country could speak in this way, using the foulest of language against a rapporteur that is highly respected."
Manila hit back against Zeid's suggestion that the president may be mentally unwell, calling his remarks an "unmeasured outburst."
"The comments of the High Commissioner bring great dishonour to the Human Rights Council and its noble endeavours", Philippine foreign minister Alan Peter Cayetano said in a statement.
"The world actually needs more Dutertes," he added.
Zeid also referred to a pending terrorism case against the UN's special rapporteur on the rights of indigenous people, Victoria Tauli Corpuz.
Manila has accused Corpuz of "alleged membership of the Communist Party of the Philippines and (the) New People's Army", Zeid said.
The New People's Army, which is waging a decades-old Maoist armed rebellion, has been designated a "terrorist organisation" by the US State Department.
Zeid said that Corpuz believes she has been targeted because of comments she made regarding the alleged killings of indigenous people in the southern region of Mindanao, where Duterte has imposed martial law in an effort to curb a jihadist threat.
"This is of course unacceptable for a special rapporteur acting on behalf of the international community whose expertise is sought by the Human Rights Council to be treated in this way", Zeid said.
"These attacks cannot go unanswered," he added.
Foreign minister Cayetano also responded on the Corpuz case, insisting there was evidence linking the UN rights experts to a banned group, without detailing the nature of the charges filed against her.
"If indeed Ms. Tauli-Corpuz and the others named in the petition are innocent as they claim they are, they should see this as an opportunity to clear their names", he said.
Duterte elected by a landslide in 2016 largely on a pledge to kill tens of thousands of criminals has boasted of killings he claims to have committed personally.
He has also sidelined many of his top domestic critics.
Most recently he has moved against the country's top judge, Maria Lourdes Sereno, who faces all-but-certain impeachment following threats by Duterte over her criticism of the drug war and crackdown on civil rights.
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