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U.N. Under-Secretary General and ESCWA Executive Secretary Rima Khalaf speaks during a news conference announcing her resignation from the United Nations in Beirut, Lebanon, March 17, 2017. REUTERS/Jamal Saidi

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BEIRUT (Reuters) - The head of the United Nation's West Asia commission resigned on Friday, after what she described as pressure from the secretary general to withdraw a report accusing Israel of imposing an "apartheid regime" on Palestinians.

The Economic and Social Commission for Western Asia (ESCWA), which comprises 18 Arab states, published the report on Wednesday and said it was the first time a U.N. body had clearly made the charge.

U.N. Under-Secretary General and ESCWA Executive Secretary Rima Khalaf announced her resignation at a news conference in Beirut.

After Secretary-General Antonio Guterres insisted on the withdrawal of the report "I submitted to him my resignation from the United Nations," she said.

The U.N. chief accepted Khalaf's resignation after asking her to remove the report from the internet, a U.N. spokesman said.

The report had concluded that "Israel has established an apartheid regime that dominates the Palestinian people as a whole". Israel fiercely rejects the accusation, often directed at it by its critics.

Israel's Foreign Ministry spokesman likened the report to anti-Semitic Nazi propaganda. The United States, Israel's main ally, said it was outraged by the report.

"It was expected that Israel and its allies would put enormous pressure on the United Nations secretary-general to renounce the report," Khalaf said.

She stood by the report, calling it the "first of its kind" from a U.N. agency that shed light on "the crimes that Israel continues to commit against the Palestinian people, which amount to war crimes against humanity".

U.S. Ambassador to the United Nations, Nikki Haley, had called for the report to be withdrawn and said on Friday that Khalaf's resignation was appropriate.

"U.N. agencies must do a better job of eliminating false and biased work, and I applaud the Secretary-General's decision to distance his good office from it," Haley said in a statement.

The report, prepared at the request of ESCWA member states, was taken off the commission's website, Khalaf said.

But she added: "Let me be clear, the report was issued ... and has impacts. The member states received copies of this report. And it is available."

The report was published without consultation with the U.N. secretariat, U.N. spokesman Stephane Dujarric had said.

"This is not about content, this is about process," Dujarric told reporters in New York on Friday.

"The secretary-general cannot accept that an under-secretary general or any other senior U.N. official that reports to him would authorise the publication under the U.N. name, under the U.N. logo, without consulting the competent departments and even himself," he said.

Israel's ambassador to the United Nations Danny Danon welcomed the resignation, calling it "long overdue".

"Anti-Israel activists do not belong in the UN," Danon said in a statement.

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".

"However, only a ruling by an international tribunal in that sense would make such an assessment truly authoritative," it added.

The report said the "strategic fragmentation of the Palestinian people" was the main method through which Israel imposed apartheid, with Palestinians divided into four groups oppressed through "distinct laws, policies and practices".

(Reporting by Ellen Francis in Beirut and Michelle Nichols in New York; editing by Andrew Roche, Bernard Orr)

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