Israel has not provided evidence to support its allegations that many employees of the main U.N. agency for Palestinian refugees are members of terrorist organizations, according to an independent review commissioned by the United Nations that was released on Monday.

The review did not address Israel’s allegation that a dozen employees of the agency, known as UNRWA, were involved in the Hamas-led assault on Israel on Oct. 7. “It is a separate mission, and it is not in our mandate,” said Catherine Colonna, the former French foreign minister who led the inquiry.

The review was announced in January, before Israel circulated claims that one in 10 of UNRWA’s 13,000 employees in the Gaza Strip was a member of Hamas or its ally, Palestinian Islamic Jihad, and that some of those employees took part in the Oct. 7 attack.

But by the time investigators started working on the review in early February, Israel had leveled those charges, giving the inquiry added significance.

Speaking at a news conference at U.N. headquarters in New York on Monday, Ms. Colonna said she wanted to be “very clear” that the question of involvement in Oct. 7 is a separate question, one that remains under internal investigation by the U.N.

While Israel has not produced evidence of ties to Hamas and other militant groups among UNRWA workers, that does not mean there is no evidence, she noted. “It’s very different,” 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.

After the Biden administration halted funding for the agency pending the results of investigations, Congress barred any money for the agency for a year, through March 2025.

The review led by Ms. Colonna 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.”

Among the countries that suspended payments over Israel’s allegations, several — including Canada, Japan and Australia — have resumed funding UNRWA, 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.

Matthew Miller, a State Department spokesman, told reporters on Monday that the Biden administration was reviewing the United Nations report and had no assessment yet of its conclusions.

“Certainly, we welcome the fact that the secretary-general has accepted the recommendations,” Mr. Miller said, adding that the United States had “long made clear that there needs to be reforms at UNRWA.”

“We have always made clear that we think the role that UNRWA plays is indispensable in providing and facilitating the delivery of humanitarian assistance — not just in Gaza, but in the broader region,” he said. “We continue to support the work that they do.”

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, Anushka Patil and Michael Crowley contributed reporting.