Washington opposes any move by United Nations bodies to recognise the Palestinians as a state, believing that this must await a negotiated Middle East peace deal.
Chris Hegadorn, the U.S. Charge d'Affaires and ranking U.S. representative to UNESCO, told The Associated Press on Thursday that the decision to pull out was linked to "the unfortunate politicization of the mandate of UNESCO, where anti-Israel bias has been a major factor and something the U.S. has been struggling to address".
The United States notified UNESCO, a UN cultural organization, of its withdrawal, the U.S. State announced on October 12.
Israeli Prime Minister Benjamin Netanyahu - who is also Israel's foreign minister - gave instructions to "prepare for Israel's exit from UNESCO parallel with the US", Netanyahu's office said in a statement on Thursday. France's U.N. ambassador, Francois Delattre, had urged the United States to remain in UNESCO this week, saying the United States "must stay committed to world affairs". He said UNESCO had "turned into a theatre of the absurd; instead of preserving history, it twists it".
Following years of tension at UNESCO, which is in the process of electing a new director-general, US State Department spokeswoman Heather Nauert announced that Washington planned to withdraw.
In a statement, Bokova said that "despite the withholding of funding, since 2011, we have deepened the partnership between the United States and UNESCO, which has never been so meaningful".
"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 said in a statement.
Earlier this year, UNESCO triggered Israel's anger after it listed Hebron, a city in the occupied West Bank, as a world heritage site in the "State of Palestine". And in 2015, Unesco adopted a resolution that criticized Israel for mishandling heritage sites in Jerusalem and condemned "Israeli aggressions and illegal measures against freedom of worship".
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.
"At the time when conflicts continue to tear apart societies across the world, it is deeply regrettable for the United States to withdraw from the United Nations agency promoting education for peace and protecting culture under attack", Bokova said.
US officials said Secretary of State Rex Tillerson made the decision and it was not discussed with other countries.
The U.S. joined UNESCO at its creation in 1945.
She paid tribute to what she said had been a meaningful relationship between UNESCO and the USA, saying: "since 2011, we have deepened the partnership between the United States and UNESCO, which has never been so meaningful".