JERUSALEM — The U.N. agency for Palestinian refugees, facing explosive allegations of ties with Hamas, is struggling to preserve its reputation and maintain its lifesaving operations in Gaza, even as Israel threatens to invade the enclave’s last refuge for displaced civilians.

Political pressure on the U.N. Relief and Works Agency mounted further on Saturday after Israel said it had uncovered a tunnel passing under UNRWA’s main headquarters in Gaza City. The Israeli military posted pictures of what it called an electrical supply hub powering a vast Hamas underground network in the area and said “large quantities of weapons” had been recovered there.

UNRWA chief Philippe Lazzarini said Saturday that the agency had no knowledge of the underground tunnel and had neither the “military and security expertise nor the capacity” to conduct military-grade inspections of the premises. Israel, he added, had not formally notified UNRWA of the findings under the compound, which staff evacuated on Oct. 12 amid Israeli bombardment.

“Oh, you knew,” COGAT, an arm of the Israeli Defense Ministry, fired back on X. “You chose to ignore the facts so you can later try and deny them.”

UNRWA has been under intense scrutiny since late last month, when Israel alleged that 12 of its employees were involved in the Oct. 7 attack led by Hamas, in which gunmen killed 1,200 people in southern Israel and took more than 250 hostages. Six of the agency’s employees were alleged to have crossed into Israel on Oct. 7 and four were involved in kidnapping Israelis, according to an intelligence dossier compiled by the Israeli government and reviewed by The Washington Post. The document did not lay out evidence against the accused.

The claims prompted the United States and Germany, UNRWA’s two biggest donors, to suspend funding along with at least 14 other countries. Amid a looming famine in Gaza, the agency is trying to stretch dwindling resources past the end of February as it pleads with Washington and others to restore more than $400 million in suspended funds.

The United States, whose contribution accounts for more than 80 percent of those funds, has conditioned their release on the findings of a U.N. investigation. Israel has not publicly detailed its claims about the employees or officially shared the allegations and supporting evidence with UNRWA, according to the United Nations.

UNRWA’s efforts in Gaza, which include feeding and housing hundreds of thousands of Palestinians, are increasingly precarious, Lazzarini said Friday. Israel’s Bank Leumi has frozen UNRWA’s account, he said, and the Israeli finance minister has threatened to cancel the agency’s tax benefits.

A month’s worth of food for 1.1 million Gazans has been held up at Israel’s southern Ashdod port, Lazzarini said, after Israeli authorities told the contractor “not to move, not to handle and not to accept any payment.”

UNRWA said it has also been unable to deliver aid to hunger-stricken Gazans in the north since Jan. 23. Israeli naval forces last week fired on a food convoy attempting to travel there, according to UNRWA Gaza director Thomas White. Israel’s military has not commented on the incident.

There is no clear alternative to UNRWA in Gaza, where more than 28,000 people have been killed during the war, according to the Gaza Health Ministry. The World Food Program said in late December that 9 in 10 people were living on less than one meal a day. Some families have resorted to eating animal feed, and many are drinking dirty water. Now, Israel has warned it is planning a military operation in Rafah, home to some 1.4 million displaced Gazans who have nowhere else to go.

State Department spokesman Vedant Patel said last week that the agency’s work in Gaza is “critical” and that Washington was looking for other donors to pick up the slack in funding.

The European Union, UNRWA’s third-largest donor, announced last month that it would not cut funding but called for an audit of the group by E.U. experts. It’s unclear whether the review can be completed before the bloc is scheduled to make its next $88 million payment at the end of this month.

Lazzarini visited Saudi Arabia, Qatar, Kuwait and the United Arab Emirates last week to seek financial and diplomatic support. He was “cautiously optimistic” that Arab states in the Persian Gulf states would help fill the funding gap, he said Friday, but he warned that UNRWA remained on the brink of collapse.

Lazzarini fired 10 of the 12 employees accused in connection with the Oct. 7 attack - the other two were dead - before investigating the Israeli claims, a move he said was necessary to demonstrate how seriously UNRWA took the allegations.

The United Nations’ internal watchdog, the Office of Internal Oversight Services, has launched an investigation, with preliminary findings expected to be presented to member states in about three weeks, Lazzarini said Friday.

While the office has worked in conflict zones in Somalia, Mali and the Democratic Republic of Congo, its investigators will face formidable challenges in an enclave under attack, according to Tamara Alrifai, an UNRWA spokesperson in Amman, Jordan.

“The fact that people are on the move constantly with multiple displacements, with very patchy telecommunications, would make it difficult to have the kind of frequency of contact that any piece of work requires, let alone an investigation of this magnitude,” she said.

UNRWA has ordered its own independent investigation into agency protocols and policies, to be led by former French foreign minister Catherine Colonna. A final report is expected to be made public by late April.

UNRWA has said it burned through its emergency financial reserves after President Donald Trump cut funding in 2018. Though President Biden restored aid in 2021, the agency has remained chronically underfunded.

Now, amid unprecedented need in Gaza, UNRWA says it is functioning month-to-month and that money is fast running out.

“Our operations across the region will be seriously compromised at the end of February,” Alrifai said. “We are trying internally a number of financial management tactics that enable services to continue throughout the month of March.”

Only 3,000 of UNRWA’s 13,000 employees in Gaza are able to work, she said, but the entire workforce there and 17,000 others across the region continue to be paid - at least for now.

Payments into pension funds could be delayed to keep paying immediate salaries, Alrifai said. The agency is also looking into a loan from U.N. headquarters in New York.

UNRWA was founded in 1949 to support Palestinians who fled or were forced from their homes during the establishment of Israel. Over the decades, the agency has taken on many functions of a state, running schools, medical centers and food assistance programs in Palestinian refugee camps that have become urban slums - not only in Gaza and the occupied West Bank but also in Lebanon, Jordan and Syria.

Israeli authorities have long accused the agency of working with, or at least turning a blind eye to, Hamas operatives in Gaza. UNRWA denies the claims.

An Israeli official, who spoke on the condition of anonymity to discuss sensitive issues, told The Post that the government is exploring “other options for bringing aid to civilians in Gaza,” but that no plans have been made.

Israeli authorities demanded last week that “responsible” U.N. agencies take on UNRWA’s mission in Gaza, echoing a long-standing demand by some Israeli politicians to dismantle the agency. But no other U.N. group operates at the scale of UNRWA or has the ability to ramp up operations to replace it, Alrifai said. And agencies cannot unilaterally change the mandate given to them by the U.N. General Assembly.

Inside Gaza, some UNRWA employees fear they could lose their livelihoods.

“Who will give us guarantees that none of us will be persecuted under any pretext that Israel and the world deem inconsistent with their standards?” said one 27-year employee, speaking to The Post on the condition of anonymity because they were not authorized to talk to the media.

Colleagues were “overcome with anxiety” about losing their salaries and felt “under constant surveillance,” the employee said.

More than 150 UNRWA employees have been killed in Gaza since Oct. 7, according to the United Nations, the largest single loss of life in the organization’s history.

Louisa Loveluck in Jerusalem, Karen DeYoung in Washington, Emily Rauhala and Beatriz Ríos in Brussels, Hazem Balousha in Amman and Hajar Harb in London contributed to this report.