"Government accusations that global human rights experts have links to the NPA seek to undermine the valuable work they do to promote accountability for rights abuses", Asia division researcher for HRW Carlos Conde said in a statement.
Zeid Ra'ad al-Hussein demanded that the Human Rights Council, which counts the Philippines among its 47 member countries, "must take a strong position" on the issue, and insisted "these attacks can not go unanswered".
'When the human rights or whoever is that rapporteur arrives, my order to you is, do not answer.'You're investigating us, fact finding?
"This is 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".
The petition claimed that rebels were trying to overthrow the government by "using acts of terror" to sow fear and panic.
Zeid Ra'ad Al Hussein said: "He needs to submit himself to some sort of psychiatric examination".
The justice ministry last month said it wanted a Manila court to declare the Communist Party of the Philippines (CPP) and its armed wing, the New People's Army (NPA), "terrorist" bodies, but made no mention of individuals it would also target.
In a petition filed in a Manila court dated February 21, 2018, seen by Human Rights Watch, the Department of Justice submitted a 55-page list that included long-time leaders of the communist movement such as Netherlands-based Jose Maria Sison, who founded the CPP in 1969, but also Victoria Tauli-Corpuz, the United Nations special rapporteur on the rights of indigenous peoples.
"The accusation against her comes after the public comments made, jointly with other special rapporteurs, in relation to the militarisation, attacks and killings of indigenous Lumad peoples by members of the armed forces in Mindanao; this accusation is considered as an act of retaliation for such comments", the experts said.More news: Walmart is launching its own meal kits in some stores
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"This action of High Commissioner Zeid Ra'ad Al-Hussein is completely uncalled for and demeans not only the Head of State of a Member-State, but tarnishes the reputation of the Office of the High Commissioner", Cayetano said.
"We are shocked that the Special Rapporteur (Tauli-Corpuz) is being targeted because of her work defending the rights of indigenous peoples", Michel Forst, the special rapporteur on the situation of human rights defenders, and Catalina Devandas Aguilar, chairperson of the Coordination Committee of the Special Procedures, said in a statement.
Carlos Conde, Philippines researcher with the New York-based Human Rights Watch, said the petition was "a virtual hit list".
But the peace process was called off in November after what Duterte called repeated attacks by the NPA during talks.
"Government accusations that worldwide human rights experts have links to the NPA seek to undermine the valuable work they do to promote accountability for rights abuses", Conde said. "Duterte is truly the No 1 terrorist in the Philippines".
An Al Jazeera investigation, however, revealed that police officers were involved in attempted killings of unarmed drug suspects.
This developed after Palace spokesman Harry Roque Jr. maintained that United Nations special rapporteur on extrajudicial executions Agnes Callamard, who has been the subject of Duterte's tirades, was "not welcome" in the Philippines.
It aims to work out if can charge Duterte for the deaths of thousands of Filipinos during the crackdown.