UN spokesman Stephane Dujarric told reporters in New York that the report was published without any prior consultation with the UN secretariat.
"The report as it stands does not reflect the views of the Secretary-General [Antonio Guterres]," said Dujarric, adding that the report itself noted that it reflects the views of the authors.
The United States, an ally of Israel, said it was outraged by the report.
"The United Nations secretariat was right to distance itself from this report, but it must go further and withdraw the report altogether," the US ambassador to the UN, Nikki Haley, said.
The Israeli Foreign Ministry spokesman, Emmanuel Nahshon, commenting on Twitter, also noted the report had not been endorsed by the UN Secretary-General.
"The attempt to smear and falsely label the only true democracy in the Middle East by creating a false analogy is despicable and constitutes a blatant lie," Israel's UN Ambassador, Danny Danon, said.
The 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".
It identified the four sets of Palestinians as: Palestinian citizens of Israel; Palestinians in East Jerusalem; Palestinians in the West Bank and Gaza Strip; and Palestinians living as refugees or in exile.
ESCWA hoped the report would inform further deliberations on the root causes of the problem in the UN, among member states, and in society, Khalaf said at an event to launch the report at ESCWA's Beirut headquarters.
It was authored by Richard Falk, a former UN human rights investigator for the Palestinian territories, and Virginia Tilley, professor of political science at Southern Illinois University.
Before leaving his post as UN special rapporteur on human rights in the Palestinian territories in 2014, Falk said Israeli policies bore unacceptable characteristics of colonialism, apartheid and ethnic cleansing.
The UN accused him of being biased against Israel.