Israel’s military has withdrawn from Gaza’s largest hospital after a two-week raid during which it said 200 militants were killed.

Palestinian residents said the troops left behind several bodies and a vast swathe of destruction.

The military has described the raid on Shifa Hospital as a major battlefield victory in the nearly six-month war but it came at a time of mounting frustration in Israel, with tens of thousands protesting against Prime Minister Benjamin Netanyahu on Sunday and demanding he do more to bring home dozens of hostages held in Gaza.

The fighting showed that Hamas can still put up resistance even in one of the hardest-hit areas.

Israel said it had largely dismantled Hamas in northern Gaza and withdrew thousands of troops late last year, leaving a security vacuum that has made it difficult to deliver desperately needed humanitarian aid.

A second shipment of food aid arrived by sea on Monday in the latest test of a new maritime route from the Mediterranean island nation of Cyprus.

One of the three boats could be seen off the coast, and Cypriot foreign minister Constantinos Kombos said they had received permission to offload. The precise mechanism of delivery was not yet clear.

The military said that among those killed at Shifa were senior Hamas operatives and other militants who had regrouped there after an earlier raid in November, and that it seized weapons and valuable intelligence.

The UN health agency said more than 20 patients died and dozens were put at risk during the raid, which brought further destruction to a hospital that had already largely ceased to function.

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Palestinians inspect the damage to a residential building (Ismael Abu Dayyah/AP)

Bassel al-Hilou said the bodies of seven of his relatives had been found in the wreckage surrounding the hospital. He said they had sought shelter at a neighbour’s house after theirs was bombed but then another strike hit the home where they were staying.

“There was a massacre in my uncle’s house,” he told The Associated Press. “The situation was indescribable.”

It was not yet known how many Palestinian civilians were killed during the raid. The military denied that its forces harmed any civilians inside the compound.

Israel has accused Hamas of using hospitals for military purposes and has raided several medical facilities. Health officials in Gaza deny those allegations.

Critics accuse the army of recklessly endangering civilians and of decimating a health sector already overwhelmed with war wounded. Palestinians say Israeli troops forced hundreds of people living near Shifa to evacuate to the south.

Rear Admiral Daniel Hagari, the top military spokesman, said Hamas and the smaller Islamic Jihad group had established their main northern headquarters inside the hospital.

He described days of close-quarters fighting and blamed Hamas for the destruction, saying some fighters barricaded themselves inside hospital wards while others launched mortar rounds at the compound.

He said the troops arrested 900 suspected militants during the raid, including more than 500 Hamas and Islamic Jihad fighters, and seized more than 3 million dollars (£2.38m) in different currencies, as well as weapons.

He denied that any civilians had been harmed by Israeli forces, saying the army evacuated more than 200 of the estimated 300 to 350 patients and delivered food, water and medical supplies to the rest.

Two Israeli soldiers were killed in the raid, the military said.

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The war has been going on for nearly six months (Ismael Abu Dayyah/AP)

Mohammed Mahdi, who was among hundreds of Palestinians to return to the area, described a scene of “total destruction”.

He said several buildings had been burned down. He counted six bodies in the area, including two in the hospital courtyard.

Another resident, Yahia Abu Auf, said there were still patients, medical workers and displaced people sheltering inside the medical compound.

He said several patients had been taken to the nearby Ahli Hospital, and that army bulldozers had ploughed over a makeshift cemetery inside the hospital compound.

“The situation is indescribable,” he said. “The occupation destroyed all sense of life here.”

Video footage circulating online showed heavily damaged and charred buildings, mounds of dirt that had been churned up by bulldozers and patients on stretchers in darkened corridors.

At least 21 patients have died since the raid began, World Health Organisation director-general Tedros Adhanom Ghebreyesus posted late on Sunday on X, formerly Twitter.

He said over a hundred patients were still inside the compound, including four children and 28 critical patients. He also said there were no nappies, urine bags or water to clean wounds, and that many patients suffered from infected wounds and dehydration.

The military had previously raided Shifa, Gaza’s largest hospital, in November, after saying Hamas maintained an elaborate command and control centre inside and beneath the compound.

It revealed a tunnel running beneath the hospital that led to a few rooms, as well as weapons it said it had confiscated from inside medical buildings, but nothing on the scale of what it had alleged prior to the raid.

The war began on October 7, when Hamas-led militants stormed into southern Israel, killing some 1,200 people, mostly civilians, and taking around 250 people hostage.

Israel responded with an air, land and sea offensive that has killed at least 32,782 Palestinians, according to Gaza’s Health Ministry. The ministry does not distinguish between civilians and combatants in its count but says women and children have made up around two-thirds of those killed.

The Israeli military says it has killed over 13,000 Hamas fighters, and blames the civilian death toll on Palestinian militants because they fight in dense residential areas.

The war has displaced most of the territory’s population and driven a third of its residents to the brink of famine. Northern Gaza, where Shifa is located, has suffered vast destruction and has been largely isolated since October, leading to widespread hunger.