In a lengthy written statement, Irina Bokova, Unesco’s director general, expressed regret at the decision and said that the American people shared the organization’s goals.
“Universality is critical to Unesco’s mission to strengthen international peace and security in the face of hatred and violence, to defend human rights and dignity,” she wrote.
In 2011, the United States stopped funding Unesco because of what was then a forgotten, 15-year-old amendment mandating a complete cutoff of American financing to any United Nations agency that accepts Palestine as a full member. Various efforts by President Barack Obama to overturn the legal restriction narrowly failed in Congress, and the United States lost its vote at the organization after two years of nonpayment, in 2013. Unesco was dependent on the United States for 22 percent of its budget, then about $70 million a year.
During the Cold War, the United States withdrew from the agency in 1984 because the Reagan administration deemed the organization too susceptible to Moscow’s influence and overly critical of Israel. President George W. Bush pledged in 2002 to rejoin the organization in part to show his willingness for international cooperation in the lead-up to the Iraq war.
Cultural organizations in the United States criticized the decision, saying Unesco played a key role in preserving vital cultural heritage worldwide.
“Although Unesco may be an imperfect organization, it has been an important leader and steadfast partner in this crucial work,” said Daniel H. Weiss, the president and chief executive of the Metropolitan Museum of Art in New York.
Ms. Bokova said she had repeatedly told members of Congress that immediate payment of the arrears was not an issue, only American political re-engagement in the organization, which she said she believed served many American interests abroad.
Ms. Bokova, in a telephone interview, said she “thought the decision was coming but why now, I don’t know, in the midst of elections” for a new director to succeed her.
France and Qatar were running neck-and-neck in the race to lead the cultural body after a third round of voting Wednesday whittled the field to five. Hamad bin Abdulaziz al-Kawari of Qatar and Audrey Azoulay of France — both former culture ministers — had 18 votes each.
Behind them in the secret ballot was an Egyptian career diplomat, Moushira Khattab, with 13 votes, and Tang Qian of China with five, according to results posted on Unesco’s website.
Ms. Bokova argued that Unesco is “so relevant to the political agenda of the American government it’s incredible,” citing its work on trying to prevent violent extremism through educational and cultural programs in the developing world. Unesco’s largest literacy program is in Afghanistan, she said, and Unesco is also working in Libya and Iraq to train teachers and preserve cultural heritage in liberated areas. It has always worked against anti-Semitism and to preserve the memory of the Holocaust, Ms. Bokova said.
Analysts said that withdrawing from the organization was a significant escalation by the United States in its criticism of United Nations bodies.
“This is another example of the Trump’s administration’s profound ambivalence and concern about the way the U.N. is structured and behaves,” said Aaron David Miller, a former Middle East negotiator and adviser in Republican and Democratic administrations.
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. 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.”
The Trump administration has made the defense of Israel on the global stage a key tenet of its foreign policy. After he was elected but before he became president, Mr. Trump made an extraordinary intervention on the world stage by criticizing the Obama administration’s decision not to block a United Nations resolution criticizing Israeli settlements. Mr. Trump has pledged to move the United States Embassy to Jerusalem from Tel Aviv and selected a pro-settlement ambassador.
Nikki R. Haley, the United Nations ambassador, has repeatedly criticized the United Nations for what she called its anti-Israel bias.
In a statement released Thursday, Prime Minister Benjamin Netanyahu of Israel praised the move by the United States and pledged to withdraw Israel from the organization as well.
“This is a courageous and ethical decision because Unesco has become a theater of the absurd and instead of preserving history, distorts it,” Mr. Netanyahu said.
For President Trump and for Mr. Netanyahu, the recognition of World Heritage sites in the Palestinian territories, like Hebron and the Church of the Nativity in Bethlehem, and the 2015 resolution and another in 2016, showed an anti-Israel bias.
The 2016 resolution condemned Israel’s “escalating aggressions” regarding a holy site in Jerusalem’s Old City, known to Muslims as al-Haram al-Sharif and to Jews as the Temple Mount. It was submitted by the Palestinians, was supported by 24 countries, with six opposing it and 26 abstaining. It referred to the holy site only using Muslim names and prompted angry reactions from Israeli politicians.