"I therefore declare and forthwith give notice. that the Philippines is withdrawing its ratification of the Rome Statute effective immediately", Duterte said in a statement.
In February, the ICC announced that it has taken the first step to probe Duterte over possible crimes against humanity in relation to his ongoing drug war, which has left as many as 20,000 people dead.
Duterte said that even if the ICC has jurisdiction over him, the accusations against him "do not fall under the enumerated grounds" of the worldwide law.
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.More news: Toyota Teases new 2019 RAV4 Ahead of New York Reveal
About 4,000 mostly urban poor Filipinos have been killed by police in the past 19 months in a brutal crackdown that has alarmed the global community.
He added: "However, President Duterte won't save himself from ICC investigation by withdrawing the Philippines as a State Party to the Rome Statute".
In response, a majority of the Philippine senators signed a resolution declaring that termination or withdrawal from the worldwide agreement is only "valid and effective" with their consent.
Duterte's bloody campaign has caused worldwide alarm and fierce criticism from some United Nations representatives, including High Commissioner for Human Rights Zeid Ra'ad al-Hussein, who on Friday said Duterte should submit himself for a psychiatric examination.
Countries can only withdraw one year after announcing their withdrawal, according to the guiding principles of the ICC.More news: Official Fantastic Beasts: The Crimes of Grindewald teaser trailer
The preliminary examination is not an investigation, the ICC said, but a process to see if there is basis to proceed with an investigation. Some have been killed in what police said were shootouts.
"The deaths occurring in the process of legitimate police operation lacked the intent to kill", said Mr Duterte. The Philippines says that is far from the case.
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 of over 3,000 alleged drug users and pushers. He said the Rome Statute that established the tribunal for heinous leaders can not be enforced in the Philippines because it has not been made public as required by law after Filipino senators ratified it in 2011. Senator Risa Hontiveros said Duterte was desperate and "may have unwittingly displayed his fear of being proven guilty".
The prime minister says the president of the Philippines was receptive to concerns he raised about human rights.
It seems that Duterte would rather withdraw from the institution.More news: Tarantino's new film adding Margot Robbie