Nauert also clarified that, in accordance with the charter of UNESCO, the decision on "the United States withdrawal will enter into force on December 31, 2018".
The U.S. move underscores the scepticism expressed by President Donald Trump about the need for the U.S.to remain engaged in multi-lateral bodies.
Mr Netanyahu said on Thursday that Israel will also withdraw from the agency, which had become a "theatre of the absurd because instead of preserving history, it distorts it".
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In a statement, the State Department said the decision will take effect December 31, 2018, and that the US will seek a "permanent observer" status instead. Prime Minister Benjamin Netanyahu has "instructed the Israeli Foreign Ministry to prepare for Israel to leave UNESCO in parallel with the USA", according to his office. It's best known for its World Heritage list.
Secretary of State Rex Tillerson gave formal notification of the USA withdrawal on the grounds of "continuing anti-Israel bias" and "mounting arrears".
Just hours after that vote, the US chose to cut its payments to UNESCO, while still maintaining its membership.
"Universality is critical to UNESCO's mission to strengthen worldwide peace and security in the face of hatred and violence, to defend human rights and dignity", she wrote.
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In 2011 the U.S. cut its funding to the agency - slashing its budget by 22 percent - in protest at its decision to grant full membership to the Palestine.
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".
Praising Trump's decision as "brave and moral", Netanyahu said he has ordered Israeli diplomats to prepare for Israel's withdrawal from the organization in concert with the Americans.
The lack of staffing and funding plans for Unesco by the U.S. have been accompanied by repeated denunciations of Unesco by senior USA officials, including U.S. ambassador to the United Nations Nikki Haley. In the USA, listed sites include the Statue of Liberty and Independence Hall, as well as national parks like Yellowstone and Yosemite.
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"At the time when the fight against violent extremism calls for renewed investment in education, in dialogue among cultures to prevent hatred, it is deeply regrettable that the United States should withdraw from the United Nations agency leading these issues", she stated. She called Washington's step a "loss to multilateralism". Under the Reagan Administration, the United States quit UNESCO in 1984, at the time accusing the agency of a pro- Soviet Union bias. In 2002, George W Bush joined UNESCO again, and in 2011, Barack Obama cut most United States funding to UNESCO due to the organization's recognition of Palestine.