"The secretary-general can not accept that an under secretary-general or any other senior United Nations official that reports to him would authorise the publication under the United Nations name, under the United Nations logo, without consulting the competent departments and even himself", Stephane Dujarric, a spokesman for United Nations chief Antonio Guterres, told reporters on Friday.
Khalaf, under-secretary general and executive secretary at the UN Economic and Social Commission for Western Asia (ESCWA), told a news conference: "The secretary general asked me yesterday morning to withdraw (the report)".
Palestinian President Mahmoud Abbas has announced that he will be granting the highest Palestinian honor to a Jordanian diplomat who stepped down on Friday as the head of a United Nations commission over pressure to withdraw a report accusing Israel of apartheid.
"Instead of succumbing to political blackmail or allowing itself to be censured or intimidated by external parties, the United Nations should condemn the acts described in the report and hold Israel responsible", said PLO Executive Committee member Hanan Ashrawi on Saturday.
"It is only normal for criminals to pressure and attack those who advocate the cause of their victims", Khalaf wrote in the resignation letter, seen by Reuters, adding that she stands by the ESCWA report.
Hanan Ashrawi, a member of the Palestine Liberation Organization's (PLO) executive committee, also criticised the decision and called on the report to be reinstated.
He confirmed Friday that Khalaf had submitted her resignation and said the report had been removed from the ESCWA website.
The ESCWA report said it had established on the "basis of scholarly inquiry and overwhelming evidence, that Israel is guilty of the crime of apartheid".
The report further accused Israel of "practices" that have fragmented Palestinians, arguing that it is the "principal method by which Israel imposes an apartheid regime".
The announcement from the office of the Palestinian president said that he had spoken personally with Rima Khalaf and thanked her for her support for the Palestinian people.
Haley described Falk as "a man who has repeatedly made biased and deeply offensive comments about Israel and espoused ridiculous conspiracy theories".