Hanan Ashrawi, a member of the Palestine Liberation Organization's executive committee, also criticized the decision and called on the report to be reinstated.
The US, which is one of Israel's key allies, also criticised the report.
A United Nations spokesman said the issue with Khalaf was not the content of the report, but a result of her failure to follow the necessary procedure before the publication.
"Anti-Israel activists do not belong in the UN", Danon said in a statement.
Khalaf, a Jordanian who headed the Beirut-based ESCWA, said she couldn't accept being subjected to pressure from Guterres to withdraw the report.
"The secretary-general can not accept that an under-secretary general or any other senior United Nations official that reports to him would authorize the publication under the United Nations name, under the United Nations logo, without consulting the competent departments and even himself".
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Israel strongly rejected the allegation made in the report and likened it to Der Sturmer, a Nazi propaganda publication, Reuters noted.
In a letter to UN Secretary-General Antonio Guterres, Khalaf said, "I do not find it surprising that such member states, who now have governments with little regard for global norms and values of human rights, will resort to intimidation when they find it hard to defend their unlawful policies and practices".
19 de marzo de 2017, 09:11Riyadh, March 19 (Prensa Latina) The Organization of Islamic Cooperation (OIC) deeply regretted that the United Nations chose to withdraw a report which - objectively - accounted for the reality of Israeli-taken policies of occupation, oppression, settlements and apartheid against Palestine-born people.
On the same day of the report's release, Khalaf said the "ignorance of the global community" in recent decades had "encouraged Israel to continue its abuses of worldwide law".
The report was still available online Friday morning US-time, but was later removed.
United States envoy to the UN Nikki Haley, who had demanded the report's withdrawal last week, said in a statement: "When someone issues a false and defamatory report in the name of the U.S., it is appropriate that the person resign".