"I regret this deeply, as it is my conviction that it is inside UNESCO and not outside it that states can best seek to overcome differences in the organization’s fields of competence," UNESCO Director-General Audrey Azoulay said in a statement.
Israel submitted a letter to UNESCO on Friday announcing its withdrawal from the UN body effective on December 31, 2018.
Israel will be following in the footsteps of the United States, which pulled out from the organization in October in light of what it referred to as "anti-Israel bias."
"In the face of disagreements among member states, which lead to votes for which they are responsible, engaging fully in the work of UNESCO makes possible sustained dialogue, cooperation and partnerships that are more necessary than ever and that I committed to support when I took office," Azoulay added.
Azoulay described UNESCO as "an institution committed to the defense of freedom of expression, the prevention of all forms of anti-Semitism and racism, which has developed a unique program of education about the Holocaust and the prevention of genocide."
Israel has been a member of UNESCO since September 16, 1949. It has ratified 18 UNESCO international conventions and has nine cultural sites on the World Heritage list.
Several prominent Israelis were honored by UNESCO, including Ivry Gitlis who served as a UNESCO Goodwill Ambassador, sculptor Dani Karavan who served as Artist for Peace, and Professor Ada Yonath who received the UNESCO-L’Oréal For Women in Science Prize in 2008.