The ICC is the world's only permanent war crimes court and aims to prosecute the worst abuses when national courts are unable or unwilling, which was opened in 2002.
Local media reported on Monday, that the country's senate had filed a resolution saying the country's withdrawal from global treaties would only be valid with its consent.
U.N. High Commissioner for Human Rights Zeid Ra'ad al-Hussein said Friday that Duterte needs to see a psychiatrist over his crude comments, including a threat to slap U.N. special rapporteur on extrajudicial killings Agnes Callamard, and the inclusion of U.N. special rapporteur on the rights of indigenous peoples Victoria Tauli-Corpuz on a list of alleged communist terrorists operating in the country.
The decision marks a stunning about-face by Duterte, who has repeatedly dared the ICC to indict him and said he was willing to "rot in jail" or go on trial to defend a war on drugs that has killed thousands of his own people.
The ICC last month started a preliminary examination to establish whether crimes against humanity may have taken place during Duterte's deadly war on drugs, and whether the ICC had jurisdiction to take on the case.
Chafing at the "baseless, unprecedented and outrageous attacks on my person", Mr Duterte said in a statement that he was serving notice that the Philippines was withdrawing its ratification of the Rome Statute.
"The deaths occurring in the process of legitimate police operation lacked the intent to kill", Duterte said.
He made no mention of the withdrawal in a speech on Wednesday.
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Duterte has been threatening to pull out of the Hague-based global tribunal since the start of his presidential term in mid-2016.
But even as early as October 13, 2016, when Duterte had only been in office less than four months, the ICC prosecutor Fatou Bensouda said in a statement that she was "deeply concerned" over reports of extra-judicial killings.
A defiant president said said last week that "not in a million years" would the ICC have jurisdiction to look into the allegations filed at the court by lawyer Jude Sabio. Some have been killed in what police said were shootouts.
Once the office of Guterres receives the letter, the Philippine government has to wait for a year before the withdrawal takes effect.
Duterte's spokesman, Harry Roque, said the ICC was "siding with the enemies of the president", while Duterte's legal counsel Salvador Panelo said the accession to the Rome Statute in 2011 was never announced in the Philippines official gazette, thus did not apply. The president renewed his verbal attacks against United Nations human rights officials who have expressed alarm over the massive killings.
Harvard Law professor and former ICC investigation and prosecution coordinator Alex Whiting said that Duterte is "deliberately and knowingly misrepresenting the facts".
"President Duterte's withdrawal from the Rome Statute is meant to escape accountability by present and even future officials for crimes committed against the people and humanity".