The Israeli military said in a statement posted to social media that it had been targeting what it described as a Hamas command center located near the hospital. “Shortly after the strike, a fire ignited in the hospital’s parking lot, most likely due to secondary explosions,” the military said. The claims could not be independently confirmed.

The strikes ignited the neat rows of tents, and video taken afterward shows firefighters and volunteers rushing to put out the blazes with hoses and buckets of water. Other footage shows emergency medical workers combing through the smoldering debris in search of casualties.

“The situation is just horrific,” said Louise Wateridge, the Gaza spokesperson for UNRWA, the U.N. agency tasked with aiding Palestinian refugees. She woke up around 3 a.m. to a call from a colleague who had been sheltering in the courtyard with the other families when the airstrike hit. He escaped his tent just in time. Not everyone was so lucky.

“There were no warnings,” Ms. Wateridge said. “Everyone was sleeping.”

Scores of families have been sheltering in the hospital parking lot for the past several months, having fled fighting elsewhere in Gaza. For some, it’s the third or fourth time they have moved in search of shelter. Al Aqsa, as central Gaza’s only functioning hospital, was thought to be relatively safe.

Before the start of the war in Gaza last October, Al Aqsa provided care to tens of thousands of patients every month. Since the fighting began, thousands of Gazans have sought safety inside the compound’s walls, even as it has been struck several times by Israeli forces.

The Israeli military has said that it was acting on information that Hamas was operating from the hospital compound, and it has repeatedly said that it tries to avoid civilian casualties. But its operations have drawn widespread criticism, including from the United Nations, which accused Israel in a report last week of a “concerted policy” to “destroy Gaza’s health care system as part of a broader assault” on Hamas.

Ms. Wateridge of UNRWA asked her colleague where he would go next now that his tent and all his remaining possessions were gone.

“He was completely silent for a moment,” she said. “Then he told me, ‘There is no safe place.’ He thought the hospital was the safest place to be.”

Raja Abdulrahim, Abu Bakr Bashir and Gabby Sobelman contributed reporting.

In July, the Houthi militia in Yemen hit an apartment building in Tel Aviv, killing one civilian. Hezbollah last week hit a nursing home north of Tel Aviv, causing damage but no casualties. Earlier in the year, Hezbollah broadcast footage that was captured by a drone that flew over sensitive installations in Haifa, seemingly without being detected.

The latest strike, on a training base south of the Israeli city of Haifa, highlighted how Hezbollah retains the ability to hurt Israel despite devastating Israeli attacks on its leadership and infrastructure. It also pointed up Israel’s defensive shortcomings, prompting the Israeli military to launch an investigation and its chief spokesman to acknowledge on Sunday: “We must provide better defense.”

One of the civilians who spotted the drone, Viki Kadosh, said she was “so frustrated, because 10 minutes before the hit, we had called in to warn about it.” Speaking on Monday to Galei Tzahal, a radio station run by the Israeli military, Ms. Kadosh said: “We spotted it flying very low, right above our home. We heard the sound it was making and immediately noticed there was something strange about it.” The Israeli military declined to comment.

The sequence of drone attacks has caused alarm in Israel as it prepares for a potential escalation with Iran. After Iran fired a barrage of ballistic missiles at Israel nearly two weeks ago, Israel is widely expected to retaliate, a response that could prompt Iran to fire more missiles and drones.

While Israel has a world-leading system to detect and intercept missiles, which can travel faster than 1,000 miles an hour, its radar systems have found it more challenging to spot unmanned aircraft, which sometimes move slower than 100 miles an hour.

Drones often contain less metal and emit less heat than high-velocity rockets and shells, meaning that they do not always set off alerts. And even when they are spotted, enemy drones are sometimes mistaken for Israeli aircraft, including small private planes, because they fly at similarly low altitudes and speeds.

“All the systems that we have in the Western world — it’s not only Israel — are built to defend or to protect the airspace from regular fighter planes and missiles,” said Ofer Haruvi, a former head of the drone department in the Israeli Air Force. “You need to redesign part of these systems so that they can see and detect and track this kind of slow-moving target.”

Israel’s Iron Dome anti-rocket system destroys the vast majority of rockets fired from Gaza and Lebanon, while its Arrow 3 interceptors were instrumental in largely blocking two massive barrages of ballistic missiles fired by Iran in April and again this month. To enhance those defenses, the United States said on Sunday that it would send Israel another anti-missile system, the Terminal High Altitude Area Defense system, or THAAD.

But Israel’s anti-drone system in particular requires improvement, experts said.

It relies mainly on radar, which is primarily designed to detect relatively large metallic objects like planes by transmitting a signal and receiving the signal’s reflected echo, according to Onn Fenig, the head of R2 Wireless, a company that designs drone detection systems and works with the Israeli military.

He said there are alternatives, including receptors that passively detect and classify the radio waves emitted by a drone, optical sensors that scan the skies for visual signs of a drone and acoustic sensors that detect the sound of a drone’s engine.

All these systems have advantages and blind spots, and Israel needs to combine them in order to build a more robust drone detection system, Mr. Fenig said.

“There’s no magic solution that, if implemented, would solve all your problems,” he said. “But we need a complete change in mind-set.”

Myra Noveck contributed reporting.

The reports had not been independently verified. The facility was to have been used for the second stage of a campaign to vaccinate children in Gaza against polio, Mr. Lazzarini said, but the drive did not take place there because of “severe damage.”

The attack, and one on a hospital nearby, was “another night of horror” and the situation in Gaza was “a never ending hell,” Mr. Lazzarini said on social media on Monday.

Palestinian health authorities say that more than 40,000 people have been killed in the enclave during Israel’s campaign against Hamas, which began after the militant group launched an attack on Israel on Oct. 7 last year in which around 1,200 people were killed.

Israel’s military did not claim responsibility for an attack on the school, but said the incident was under review.

In recent months, Israel’s forces have conducted dozens of airstrikes on schools that in the past year have been turned into shelters for people displaced by the war. In almost every case, it has said that the compounds were being used by Hamas, though it has not provided evidence in support of the claims.

Hundreds of people have been killed in the attacks, which have been criticized as a violation of international law by the United Nations and some governments.

The vaccination campaign restarted on Monday, a month after nearly 560,000 children under the age of 10 were given the first dose of the vaccination against the disease. Aid agencies plan to administer second doses across Gaza over the next two weeks. Israel and Hamas have agreed to pause fighting for several hours a day in areas where vaccines are being administered.

This time, UNRWA said in a statement that it aimed to reach 590,000 children under the age of 10 in less than two weeks, providing vitamin A in addition to the polio vaccine to support the health of children “living in extremely dire hygiene and sanitation conditions.”

The campaign will be run in coordination with Israel’s military to ensure that “the population will be able to safely reach the medical centers where the vaccinations will be given,” according to a statement by COGAT, the Israeli military agency that oversees policy for the Palestinian territories and liaises with international relief organizations.

More than 1,500 Israelis have been killed in the conflict, mostly during Hamas’s attack on Oct. 7. More than 40,000 Palestinians have been killed in Israel’s counterattack, including thousands of children.

An UNRWA spokeswoman, Louise Wateridge, said that, while the campaign was critical, “the children will inevitably return straight back into the dangerous and inhumane conditions they came from.”

The COGAT statement did not mention UNRWA. The agency, which has had more than 200 of its Palestinian employees killed during the war, has been key to efforts to provide shelter, food and other basic services during the war, but Israel accuses it of aiding Hamas. Israel’s parliament has taken steps toward passing a bill branding UNRWA as a terrorist organization.

“The inviolability of U.N. premises must be respected at all times,” Mr. Guterres said in a statement on social media on Sunday. “Attacks against peacekeepers are in breach of international law and may constitute a war crime.”

The Israeli military said that its soldiers had entered the peacekeeping base as they tried to flee from Hezbollah missile fire and were in contact throughout the episode with the U.N. peacekeeping mission, known as UNIFIL.

The mission came under Israeli fire several times last week, and Israeli officials have called on the United Nations to pull its peacekeeping forces back. Prime Minister Benjamin Netanyahu said on Sunday that the United Nations’ refusal to do so “makes them hostages of Hezbollah,” the armed Lebanese group that the Israeli military has been targeting in a weekslong air and ground offensive.

“This endangers both them and the lives of our soldiers,” Mr. Netanyahu said, in a message directed at Mr. Guterres.

The U.N. force has rejected Israel’s calls to leave its positions in southern Lebanon. Mr. Guterres does not have authority over UNIFIL, whose presence is mandated by the U.N. Security Council.

United Nations peacekeeping forces have been in southern Lebanon since 1978. The mission includes over 10,000 civilian and military personnel from 50 countries who are assigned to prevent border violations between Lebanon and Israel over a 75-mile stretch referred to as the Blue Line.

In an overnight call with Israeli Minister of Defense Yoav Gallant, U.S. Defense Secretary Lloyd J. Austin III “reinforced the importance of Israel taking all necessary measures to ensure the safety and security of UNIFIL forces and Lebanese Armed Forces,” the Pentagon press secretary, Maj. Gen. Pat Ryder, said in a statement.

The episode on Sunday was the latest in a series of Israeli challenges to the peacekeeping force since invading southern Lebanon in late September.

On Saturday, UNIFIL reported that Israeli soldiers had blocked peacekeepers’ passage through an area northeast of Ramyah, prompting the mission to issue its fourth warning in recent days to Israel and other parties “to steer clear of the mission’s premises and operations.”

“UNIFIL’s mandate provides for its freedom of movement in its area of operations,” it said.