The state WAM news agency issued an official statement on Wednesday bearing the name of the UAE leader, Shaikh Zayed bin Sultan al-Nahayan, saying the centre had been closed for religious intolerance.
"Having learned that the centre took part in a dialogue that flouts the principles of religious tolerance, His Highness ordered its immediate closure," the statement said.
"Shaikh Zayed has always been an advocate of religious tolerance and peaceful coexistence among peoples," sponsoring charity projects irrespective of the ethnic or religious affiliation of recipients, it added.
The Zayed Centre for Coordination and Follow-Up (ZCCF) is affiliated to the Arab League and has been operating here since 1999, hosting speakers from around the world and issuing dozens of publications.
Former US President Jimmy Carter and former Vice President Al Gore were the most prominent of many US figures who have spoken at the centre.
The UAE-funded ZCCF has repeatedly complained that US and other Western charges of anti-Semitism were part of an Israeli-inspired campaign against the centre.
"Jewish institutions" fuelled the campaign after the centre hosted figures they considered "anti-Semitic," a ZCCF official told AFP in April.
Arab media had reported the centre might be shut down, prompting several Arab intellectuals to put their names to a petition opposing any such move.