Jordanian UN official Rima Khalaf announced her resignation on Friday, saying the secretary general had asked her to withdraw a report in which she accused Israel of being an "apartheid state."
Her resignation comes after the United States on Wednesday demanded that UN Secretary General Antonio Guterres withdraw the UN Economic and Social Commission for Western Asia (ESCWA) report.
"The secretary general asked me yesterday morning to withdraw (the report). I asked him to rethink his decision, he insisted, so I submitted my resignation from the UN," Khalaf, under-secretary general and ESCWA executive secretary told a news conference on Friday.
The report said it had established on the "basis of scholarly inquiry and overwhelming evidence, that Israel is guilty of the crime of apartheid."
"However, only a ruling by an international tribunal in that sense would make such an assessment truly authoritative," it added.
The authors of the report concluded that "Israel has established an apartheid regime that systematically institutionalises racial oppression and domination of the Palestinian people as a whole."
Khalaf had said the report was the "first of its type" from a UN body that "clearly and frankly concludes that Israel is a racist state that has established an apartheid system that persecutes the Palestinian people."
Israel's foreign ministry, however, likened the report to Der Sturmer, a Nazi propaganda publication that was strongly anti-Semitic.
Israeli UN Ambassador Danny Danon, meanwhile, denounced the report, calling it a "blatant lie" and an "attempt to smear and falsely label the only true democracy in the Middle East."
ESCWA comprises 18 Arab states in Western Asia and aims to support economic and social development in member states, according to its website.
The report was prepared at the request of member states and was authored by former UN human rights investigator for the Palestinian territories Richard Falk and political science professor Virginia Tilley.
But UN Spokesman for the Secretary-General Stephane Dujarric said the report was published without any prior consultation with the UN Secretariat.