Daniel Meron, Israel's ambassador to the United Nations in Geneva, said the Soroka Hospital in Beersheba was a civilian facility.
In a video on X filmed outside the WHO's headquarters, he demanded a condemnation from the UN health agency.
A few hours later, WHO chief Tedros Adhanom Ghebreyesus issued a statement saying the reports on attacks on health in the conflict between Iran and Israel were "appalling", citing the hospital.
The Soroka Hospital was left in flames by a bombardment that Iran said targeted a military and intelligence base.
In his video, Meron was standing at the road entrance to the WHO's offices in Geneva, with the main building visible in the background.
"I'm here with a clear message to the WHO, to the director general of the WHO, Dr Tedros," Meron said.
"A few hours ago, a ballistic missile was shot from Iran directly at the main hospital in the south of Israel, the Soroka Hospital. Dozens of people were wounded and hundreds were evacuated from this hospital.
"It is not a military site. It is a civilian hospital... the selective silence of the WHO is deafening.
"They must condemn the shooting of ballistic missiles and the targeting from Iran at civilian targets in Israel."
The WHO has repeatedly mentioned damage to healthcare infrastructure in the Gaza Strip since the start of the war in the Palestinian territory, triggered by the October 7, 2023 attacks by Hamas.
On Tuesday, the WHO said only 17 of Gaza's 36 hospitals were currently minimally to partially functional.
In a message later Thursday on X, Tedros said: "The escalation of hostilities between Israel and Iran is putting health facilities and access to health care at risk. The reports on the attacks on health so far are appalling."
He cited "this morning's attack on Soroka Medical Centre", and a hospital in Kermanshah in Iran being "impacted by a nearby explosion".
"We call on all parties to protect health facilities, health personnel and patients at all times," said Tedros.
WHO's director for Europe Hans Kluge said he was "deeply disturbed to learn of the attack on Soroka Hospital", having visited it following the October 7, 2023 attacks.
"Hospitals and health workers must never be targets -- under any circumstances," Kluge said.
Israel is in the WHO's Europe region.
Israel minister says Iran leader 'can no longer exist' after hospital hit
Jerusalem (AFP) June 19, 2025 -
Israel's defence minister warned that Iran's supreme leader "can no longer be allowed to exist" after a hospital was hit in an Iranian missile strike on Thursday, spiking tensions in the week-old war.
As President Donald Trump dangled the prospect of US involvement, Soroka Hospital in the southern city of Beersheba was left in flames by a bombardment that Iran said targeted a military and intelligence base.
Meanwhile Russia, an Iranian ally, told the United States that joining the conflict would be an "extremely dangerous step".
Israel, fearing Iran is on the verge of developing a nuclear weapon, launched air strikes against its arch-enemy last week, triggering deadly exchanges.
Prime Minister Benjamin Netanyahu said Iran would "pay a heavy price" for the hospital strike, while Defence Minister Israel Katz issued a stark warning for supreme leader Ayatollah Ali Khamenei.
"Khamenei openly declares that he wants Israel destroyed -- he personally gives the order to fire on hospitals," Katz told reporters.
"He considers the destruction of the state of Israel to be a goal. Such a man can no longer be allowed to exist."
The latest escalation came on the seventh day of deadly exchanges between the two countries that have plunged the region into a new crisis, 20 months into the Gaza war.
Hospital director Shlomi Codish said 40 people were injured at the Soroka, where an evacuated surgical building was hit leaving smoke billowing.
"Several wards were completely demolished and there is extensive damage across the entire hospital," he told journalists at the site.
World Health Organization director-general Tedros Adhanom Ghebreyesus called attacks on health facilities "appalling", while UN rights chief Volker Turk said civilians were being treated as "collateral damage".
- 'People are really panicking' -
People fleeing the attacks on Iran described frightening scenes and difficult living conditions, including food shortages and limited internet access.
"Those days and nights were very horrifying... hearing sirens, the wailing, the danger of being hit by missiles," University of Tehran student Mohammad Hassan told AFP, after returning to his native Pakistan.
"People are really panicking," a 50-year-old Iranian pharmacist who did not want to be named told AFP at the Kapikoy crossing on the Turkish border.
"Yesterday the internet stopped and two major banks were hacked so people couldn't access their money. And there's not even enough food."
Khamenei has rejected Trump's demand for an "unconditional surrender", despite the president's claim that Iran wants to negotiate.
Trump has been deliberately vague about joining the conflict, saying Wednesday: "I may do it, I may not do it. I mean, nobody knows what I'm going to do.
"The next week is going to be very big," he added, without further details.
Any US involvement would be expected to involve the bombing of a crucial underground Iranian nuclear facility in Fordo, using specially developed bunker-busting bombs.
The White House said Trump would receive an intelligence briefing on Thursday, a US holiday. Top US diplomat Marco Rubio is set meet his British counterpart for talks expected to focus on the conflict.
The Wall Street Journal reported that Trump had told aides on Tuesday he had approved attack plans but was holding off to see if Iran would give up its nuclear programme.
The US president had favoured a diplomatic route to end Iran's nuclear programme, seeking a deal to replace the 2015 agreement he tore up in his first term.
But since Israel unleashed the campaign against Iran last week, Trump has stood behind the key US ally.
In Moscow, Russian foreign ministry spokeswoman Maria Zakharova told reporters that any US military intervention would have "truly unpredictable negative consequences".
- Nuclear sites -
On Thursday, Israel said it had carried out dozens of fresh raids on Iranian targets overnight, including the partially built Arak nuclear reactor and a uranium enrichment facility in Natanz.
The Israeli military said the Arak site in central Iran had been hit "to prevent the reactor from being restored and used for nuclear weapons development".
There was a "near-total national internet blackout" in Iran on Wednesday, a London-based watchdog said, with Iran's Fars news agency confirming tighter internet restrictions after initial curbs imposed last week.
An Israeli military official, who asked not to be named, said Wednesday that Iran had fired around 400 ballistic missiles and 1,000 drones since the conflict began on Friday.
Iranian strikes have killed at least 24 people and injured hundreds since they began, Netanyahu's office said on Monday.
Iran said Sunday that Israeli strikes had killed at least 224 people, including military commanders, nuclear scientists and civilians.
Iran had been enriching uranium to 60 percent -- far above the 3.67-percent limit set by the 2015 deal, but still short of the 90 percent needed for a nuclear warhead.
Israel has maintained ambiguity on its own arsenal, but the Stockholm International Peace Research Institute says it has 90 nuclear warheads.
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