But by the time investigators started working on the review in early February, it had taken on additional significance: Israel had accused about a dozen employees of the agency, which employs about 13,000 Palestinians in Gaza, of involvement in the Oct. 7 Hamas-led attacks on Israel or their aftermath. Israel had also said that one in 10 UNRWA employees in Gaza was a member of Hamas or its ally, Palestinian Islamic Jihad.

Speaking at a news conference at U.N. headquarters in New York on Monday, Catherine Colonna, the former French foreign minister who led the inquiry, said she wanted to be “very clear” that her review did not address the allegations that some UNRWA staff members were involved in the Oct. 7 attacks. That question remains under internal investigation by the U.N.

“It is a separate mission, and it is not in our mandate,” she said.

More than a dozen countries, including the United States, suspended funding to UNRWA in light of the allegations. The United Nations fired 10 of the 12 employees accused in the attack while pleading with donor countries to restore funding at a time when the majority of Gazans depend on the group for food and shelter. It also announced an internal investigation along with the independent external review, which was made public on Monday.

The review said that UNRWA had long shared lists of its employees with Israel, but that the Israeli government had not flagged any concerns about agency employees since 2011.

“Israel made public claims that a significant number of UNRWA employees are members of terrorist organizations,” the report said. “However, Israel has yet to provide supporting evidence of this.”

In a statement on Monday, Oren Marmorstein, a spokesman for the Israeli foreign ministry, said, “Hamas has infiltrated UNRWA so deeply that it is no longer possible to determine where UNRWA ends and where Hamas begins.”

“This is not what a genuine and thorough review looks like,” he added. “This is what an effort to avoid the problem and not address it head on looks like.”

Amid calls from Israel to shutter the agency, the report commissioned by the United Nations said UNRWA remained “pivotal in providing life-saving humanitarian aid and essential social services,” adding that “UNRWA is irreplaceable and indispensable to Palestinians’ human and economic development.”

Still, the report found that despite “robust” guidelines to ensure its neutrality, there were weaknesses in their implementation because of problems in the agency’s vetting processes, its internal investigations and restrictions on its ability to prevent armed groups from using its facilities for military purposes.

The report said the agency “lacks the support of intelligence services to undertake efficient and comprehensive vetting.”

A lack of resources had slowed the agency’s investigations into alleged breaches of neutrality, “limiting UNRWA’s ability to attract, hire, train and retain suitable, experienced and qualified investigators,” the report said.

The report added that there had been instances when agency employees had publicly expressed political views, its schools had used textbooks with “problematic content” and some of its facilities had been used for “political or military purposes.” The report did not elaborate, but said that breaches of neutrality “could include the discovery of weapons, cavities and tunnel openings, military activities or incursions.”

The review offered recommendations for protecting the agency’s neutrality, including additional screening and training of staff members, and closer cooperation with host countries and Israel in sharing employee rosters.

Stéphane Dujarric, spokesman for the U.N. secretary general, António Guterres, said on Monday that Mr. Guterres had accepted the report’s recommendations and appealed for donors “to actively support UNRWA, as it is a lifeline for Palestine refugees in the region.”

Canada and Sweden — among the countries that suspended payments over Israel’s allegations — resumed funding UNRWA last month, citing the spiraling humanitarian catastrophe in Gaza and steps taken by the agency to improve accountability. The United States has said it would wait for the results of U.N. investigations before deciding whether to resume donations to UNRWA.

UNRWA was created to provide aid to Palestinians across the Middle East whose families fled or were forced from lands during the wars surrounding Israel’s creation in 1948. Since Hamas won Palestinian elections in Gaza in 2006 and ousted a rival faction from the enclave a year later, the group ceded many of its civil responsibilities to UNRWA.

Israel has alleged that UNRWA is fundamentally compromised, and Prime Minister Benjamin Netanyahu has called for it to be closed and replaced “with responsible international aid agencies.”

Michael Levenson and Anushka Patil contributed reporting.