The head of a Lebanon-based United Nations agency that promotes development in Arab countries has resigned, after refusing to withdraw a controversial report that concludes that Israel has established an "apartheid regime."

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The report for the United Nations Economic and Social Commission for Western Asia (ESCWA), which comprises 18 Arab states, concluded that "Israel has established an apartheid regime that dominates the Palestinian people as a whole".

The accusation - often directed against Israel by its critics - has never before been made by a United Nations body.

Open gallery view United Nations Secretary-General Antonio Guterres speaks to reporters during a news conference, Wednesday, Feb. 1, 2017 at United Nations headquarters. Credit: Mary Altaffer/AP

Earlier Friday, UN Secretary-General Antonio Guterres asked that the report be remove from the agency's website, a UN official said on Friday.

Rima Khalaf, a Jordanian who heads the Beirut-based ESCWA, announced her resignation at a hastily-arranged press conference in the Lebanese capital Friday.

Israel praised the move, with its envoy to the UN, Danny Danon, thanking Guterres and saying in a statement that "the time has come to put an end to those using their status within the UN to promote anti-Israel activity.

"Khalaf has for years worked to harm Israel and to promote the BDS and she should have left her role a long time ago."

Khalaf stood by the report, calling it the "first of its kind" from a UN agency that sheds light on "the crimes that Israel continues to commit against the Palestinian people, which amount to war crimes against humanity/"

The report, which Khalaf had said had been prepared at the request of ESCWA member states, was no longer visible on the commission's website on Friday.

UN spokesman Stephane Dujarric said on Wednesday the report was published without prior consultation with the UN secretariat.

Israel's foreign ministry spokesman likened the report to a Nazi propaganda publication that was strongly anti-Semitic and described it as "despicable and a blatant lie".

The United States, Israel's main ally, said it was outraged by the report.