She accused the "powerful member states" of the United Nations of attacking "those who advocate the cause of their victims".
Last month, Nasrallah warned that Hezbollah would put up fierce resistance in any future confrontation with Israel should the United States give it the green light to attack it inside Lebanon.
Palestinian Minister of Foreign Affairs Riyad al-Maliki also voiced deep regrets that Khalaf was forced to resign and expressed his "unequivocal objection" over the removal of the report.
"It was expected, naturally, that Israel and its allies would exercise huge pressure on the United Nations secretary-general to distance himself from the report and to ask for it to be withdrawn", she said.
She also called on UN Secretary General Antonio Guterres "to do what is right, reinstate the ESCWA report and undertake serious and concrete measures to hold Israel accountable for its persistent violations of global law and human rights".
The accusation-often directed at Israel by its critics-is fiercely rejected by Israel.
Khalaf stood by the report, calling it the "first of its kind" from a United Nations agency that sheds light on "the crimes that Israel continues to commit against the Palestinian people, which amount to war crimes against humanity".
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Khalaf left her post after UN Secretary General Antonio Guterres ordered that the report be taken off the organization's website.
US UN envoy Nikki Haley praised Guterres for killing the report.
The report was still available online Friday morning US-time, but was later removed.
"It's only normal for the criminal to attack those defending the cause of his victims, but I can not accept being subjected to such pressures", she told reporters in Beirut, quoting from her resignation letter.
USA 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 United States, it is appropriate that the person resign".
"UN 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. "Let me be clear, the report was issued... and has impacts".