TEL AVIV—At least 12 employees of the U.N.’s Palestinian refugee agency had connections to Hamas’s Oct. 7 attack on Israel and around 10% of all of its Gaza staff have ties to Islamist militant groups, according to intelligence reports reviewed by The Wall Street Journal.

Six United Nations Relief and Works Agency workers were part of the wave of Palestinian militants who killed 1,200 people in the deadliest assault on Jews since the Holocaust, according to the intelligence dossier. Two helped kidnap Israelis. Two others were tracked to sites where scores of Israeli civilians were shot and killed. Others coordinated logistics for the assault, including procuring weapons.

The information in the intelligence reports—based on what an official described as very sensitive signals intelligence as well as cellphone tracking data, interrogations of captured Hamas fighters and documents recovered from dead militants, among other things—were part of a briefing given by Israel to U.S. officials that led Washington and others to suspend aid to Unrwa.

Intelligence estimates shared with the U.S. conclude that around 1,200 of Unrwa’s roughly 12,000 employees in Gaza have links to Hamas or Palestinian Islamic Jihad, and about half have close relatives who belong to the Islamist militant groups. Both groups have been designated as terrorist organizations by the U.S. and others. Hamas has run Gaza since a 2007 coup.

“Unrwa’s problem is not just ‘a few bad apples’ involved in the October 7 massacre,” said a senior Israeli government official. “The institution as a whole is a haven for Hamas’ radical ideology.”

An Unrwa spokesperson on Monday declined to comment, saying an internal U.N. investigation into the agency was under way.

In the aftermath of Oct. 7, as Israel has waged war against Hamas in Gaza, Unrwa has emerged as one of the loudest voices decrying the impact of the fierce fighting on Palestinians in the enclave, where authorities say more than 26,000 people have been killed. Unrwa says at least 152 of its own staff have been killed in the conflict.

The agency is also the main pillar of operations to move food aid, medicine and other humanitarian supplies into Gaza.

The vast majority of Unrwa’s 30,000 staff across the Middle East are Palestinian, and Israel and some in the U.S. have long accused it of nurturing anti-Israeli sentiment in crowded refugee camps that have been important recruiting grounds for militant groups, including Hamas.

The Trump administration suspended funding for Unrwa in 2018, saying the agency’s mission was fundamentally misguided. The Biden administration renewed funding in 2021.

The Oct. 7 intelligence reports seen by the Journal identified an Unrwa Arabic teacher who the reports said was also a Hamas militant commander and took part in a terrorist attack on Kibbutz Be’eri, where 97 people were killed and about 26 people were kidnapped and taken as hostages to Gaza.

Another Unrwa employee, described in the dossier as an Unrwa social worker, played a role in absconding with the body of a dead Israeli soldier, which was taken to Gaza, the reports said. He also coordinated trucks and munitions distributions for Hamas before being killed.

A person familiar with the dossier said that after U.S. officials were briefed on the intelligence material, they alerted Unrwa, which put out a statement announcing the allegation that some of its employees were linked to the attacks and saying it had fired the employees involved. It provided no details, and didn’t say how many employees were involved.

On Sunday, U.N. Secretary-General António Guterres said he was personally horrified by the allegations.

Unrwa commissioner-general Philippe Lazzarini criticized Western nations for pausing aid at a time when Gaza is facing a humanitarian crisis as the war between Hamas and Israel rages. Guterres also implored nations to not suspend humanitarian aid.

It is “immensely irresponsible to sanction an agency and an entire community it serves because of allegations of criminal acts against some individuals,” Lazzarini said.

Unrwa looks after more than 5 million Palestinians in densely-packed refugee neighborhoods across the Middle East, including the West Bank, Jordan, Syria and Lebanon. But its biggest operations are in Gaza, where it looks after an estimated 80% of the local population and runs hundreds of schools and scores of clinics.

Israel says it has documented deepening ties between Unrwa and Hamas since the militant group cemented its hold on Gaza in 2007. Unrwa has admitted to finding Hamas weapons stored in schools and Israel has repeatedly said Hamas tunnels run under and through Unrwa buildings as well as other civilian facilities. The former head of Unrwa’s union in Gaza was fired in 2017 after Israel found out he had been elected to Hamas’ top political leadership.

The dossier is the most detailed look yet at the widespread links between the Unrwa employees and militants. It offers telling details regarding the events of Oct. 7.

A math teacher belonging to Hamas was close enough to a female hostage in Gaza that he took a picture of her. Another teacher was carrying an antitank missile the night before the invasion.

One Unrwa employee set up an operations room for Palestinian Islamic Jihad on Oct. 8, the day after the attack. Three other employees, including another Arabic teacher at an Unrwa school, received a text from Hamas to arm themselves at a staging area close to the border the night before the attack. It was unclear whether they went.

A different elementary school teacher did cross into Israel and went to Reim, a district where a kibbutz, an army base and a music festival were attacked.

One of the intelligence reports seen by the Journal said a 13th Unrwa employee, who didn’t have a discernible affiliation with a terror group, also entered Israel. Hundreds of Gazan civilians flooded across the border as part of the Hamas-led attack, Israel says.

Teachers make up nearly three-quarters of Unrwa’s Gaza-based local staff. Unrwa schools, which use textbooks approved by the Palestinian Authority, have come under fire for using materials that allegedly glorify terrorists and promote hatred of Israel. Unrwa says it has taken steps to address problematic content, but a 2019 U.S. Government Accountability Office report said that measures haven’t always been implemented.

Since Oct. 7, Hamas has stolen more than $1 million worth of Unrwa supplies, including fuel and trucks, according to the intelligence report. The intelligence assessment alleges that Hamas operatives are so deeply enmeshed within the Unrwa aid-delivery enterprise as to coordinate transfers for the organization.

Write to David Luhnow at