Rima Khalef, an Under-Secretary General for the organisation, led the report published by the Economic and Social Commission for Western Asia (ESCWA), which concluded Israel is a “racist state”.
Ms Khalef, a Jordanian, said she resigned after the report was taken down from the ESCWA’s website after two days and UN Secretary General Antonio Guterres distanced himself from its findings, saying it reflected her personal views.
“We expected of course that Israel and its allies would put huge pressure on the secretary general of the UN so that he would disavow the report, and that they would ask him to withdraw it,” she told the Agence France Presse news agency.
In her resignation letter, Ms Khalef acknowledged she had only two weeks of her contract left to serve, but said: "I cannot withdraw yet another well-researched, well-documented UN work on grave violations of human rights, yet I know that clear instructions by the Secretary-General will have to be implemented promptly.
"A dilemma that can only be resolved by my stepping down to allow someone else to deliver what I am unable to deliver in good conscience. I know that I have only two more weeks to serve; my resignation is therefore not intended for political pressure. It is simply because I feel it my duty towards the people we serve, towards the UN and towards myself, not to withdraw an honest testimony about an ongoing crime that is at the root of so much human suffering."
The ESCWA is based in Lebanese capital Beirut and promotes economic and social development in 18 Arab countries.
Its report, which is no longer visible on the website, concluded on the “basis on scholarly enquiry and overwhelming evidence, that Israel is guilty of the crime of apartheid.”
Italso encouraged governments around the world to support the boycott, divestment and sanctions movement against Israel.
Ms Khalef was praised for her courage by Palestinian President Mahmoud Abbas.
Mr Abbas had spoken to Ms Khalef by phone and given her Palestine's Medal of the Highest Honor in recognition of her “courage and support” for his people, local media reported.
Israel immediately condemned the report, which was co-authored by Richard Falk, who has courted controversy in the past by suggesting the 9/11 attacks could have been a conspiracy involving the west.
“The attempt to smear and falsely label the only true democracy in the Middle East by creating a false analogy is despicable and constitutes a blatant lie,” Israel's UN Ambassador Danny Danon said in a statement.
America's UN ambassador Nikki Haley also called for the report to be withdrawn , describing it as “anti-Israel propaganda”.
“The United States stands with our ally Israel and will continue to oppose biased and anti-Israel actions across the UN system and around the world,” he said.
A UN spokesman said the organisation did not have a problem with the content of the report but rather with Ms Khalef’s failure to follow procedure prior to publication.
"The secretary-general cannot accept that an under secretary-general or any other senior UN official that reports to him would authorise the publication under the UN name, under the UN logo, without consulting the competent departments and even himself," said Stephane Dujarric, a spokesman for UN chief Antonio Guterres.