Since 2011, United States arrears to the organization have reached about $600 million, Ms. Bokova said, but she had told members of Congress repeatedly that immediate payment was not an issue, only American political re-engagement in the organization, which she believes serves many American interests overseas.
The Trump administration has been preparing for a likely withdrawal for months, and a decision was expected before the end of the year, according to U.S. officials.
Netanyahu accused UNESCO of "becoming a Theater of Absurd because instead of preserving history, it twists it".
It will establish an observer mission at the Paris-based organisation to replace its representation, the state department said.
Hours later, Prime Minister Benjamin Netanyahu said Israel would quit too, calling the USA decision "brave and moral".
In July, Unesco declared the ancient and hotly contested core of Hebron, in the Israeli-occupied West Bank, as a Palestinian World Heritage site in danger, a decision sharply criticized by Israel and its allies.
Israel on Thursday welcomed USA pulling out of the UN's cultural organization, announcing the Jewish state was considering a similar move due to the body's "anti-Israel" bias.
Today the Trump administration announced the United States will leave UNESCO, the United Nations development agency, over the organization's alleged "anti-Israel bias".
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"UNESCO is about promoting our ideals and values through culture, education and science", France's United Nations ambassador Francois Delattre told reporters in NY, adding that "we need an America that stays committed to world affairs".
President George W. Bush announced America's return in 2002, but relations soured again in 2011 when Washington pulled the plug on funding to the body after its members voted to admit Palestine as a full member.
"Universality is critical to UNESCO's mission to strengthen global peace and security in the face of hatred and violence, to defend human rights and dignity", she said in a statement.
In October, Israel suspended its co-operation over a draft resolution referring to the Old City of Jerusalem as part of "the cultural heritage of Palestine".
He said he has ordered Israeli diplomats to prepare Israel's withdrawal from the organisation in concert with the Americans. This is a loss to the United Nations family.
The outgoing head of UNESCO, Irina Bokova, called the USA withdrawal a "loss to multilateralism", while UN Secretary General Antonio Guterres said through a spokesman that he "regrets this development deeply".
UNESCO is a specialized agency in the United Nations that encourages worldwide peace and security through education, science, culture and communication.