Bodies covered in white lay on the ground in a courtyard of the facility. A man in a baseball cap leaned over one body bag, clasping a dust-covered hand that protruded.
The feet of another corpse poked from under a blanket bearing the picture of a large teddy bear.
In Rafah, witnesses reported intense air strikes near the crossing with Egypt, and smoke was seen rising over the city.
Other strikes occurred in north Gaza, witnesses said.
Israeli troops on Tuesday seized and closed the Palestinian side of the Rafah crossing – through which all fuel passes into Gaza – after ordering residents of eastern Rafah to evacuate.
The army said on Saturday troops were engaged in “operational activity” at the crossing, where they fought against “armed terrorists” and found “numerous underground tunnel shafts”.
While mediation efforts towards a truce and hostage release appear to stall, Hamas’ armed wing released a video of a captive seen alive in Gaza – the third such footage released in less than a month.
The man is seen speaking in the 11-second clip, which is superimposed with text in Arabic and Hebrew that reads: “Time is running out.”
The new evacuation order for eastern Rafah, posted on social media platform X by military spokesman Avichay Adraee, said the designated areas had “witnessed Hamas terrorist activities in recent days and weeks”.
The war began with Hamas’ unprecedented October 7 attack on Israel, which resulted in the deaths of more than 1,170 people, mostly civilians, according to an Agence France-Presse tally of Israeli official figures.
During their attack, militants also seized hostages. Israel estimates 128 of them remain in Gaza, including 36 whom the military says are dead.
Israel’s retaliatory offensive has killed at least 34,971 people in Gaza, mostly women and children, according to the Hamas-run territory’s health ministry.
A US State Department report on Friday said it was “reasonable to assess” that Israel violated norms on international law in its use of weapons from the United States but it did not find enough evidence to block shipments.
The State Department submitted its report two days after President Joe Biden publicly threatened to withhold certain bombs and artillery shells if Israel goes ahead with an all-out assault on Rafah, where the United Nations said 1.4 million had been sheltering.
Hamas in a statement said Israel’s “continued control” and closure of the Rafah crossing exacerbated the “humanitarian catastrophe” in the besieged territory.
Israeli Prime Minister Benjamin Netanyahu has pledged to “eliminate” Hamas battalions in Rafah, after the army in January said it had dismantled the Hamas command structure in northern Gaza.
But on Saturday, Adraee said Hamas “is trying to rebuild” there, and ordered evacuations from the north’s Jabalia refugee camp and Beit Lahia areas.
After rising criticism from Washington over the civilian impact of Israel’s war against Hamas, the threat to withhold weapons was the first time Biden raised the ultimate US leverage over Israel – its military aid which totals US$3 billion annually.
UN Secretary-General Antonio Guterres said on Friday that Gaza risked an “epic humanitarian disaster” if Israel launched a full-scale ground operation in Rafah.
The army said it reopened Kerem Shalom crossing near Rafah on Wednesday, but aid agencies cautioned that getting assistance through the militarised area remained extremely difficult.
Israel has said its Erez crossing into northern Gaza remains open.
On Friday, the White House said it did not yet see a “major ground operation” in Rafah but was watching the situation “with concern”.
Biden’s administration had already paused delivery of 3,500 bombs as Israel appeared ready to attack Rafah.
More than 100,000 people fled the city after the initial evacuation order, the UN said on Friday.
Israel on Saturday gave a figure of 300,000, as more Rafah residents piled water tanks, mattresses and other belongings onto vehicles and prepared to flee again.
Malek al-Zaza, with a trim grey beard, said he has been displaced three times now during the war and found “no food” and “no water” in central Gaza’s Nuseirat camp, where he has returned.
“We only have God looking out for us,” he said.
Israel said it had delivered 200,000 litres of fuel to Gaza on Friday through Kerem Shalom – the amount the United Nations says is needed every day to keep aid trucks moving and hospital generators working.
Reiterating his calls for a ceasefire, Guterres said: “We are actively engaged with all involved for the resumption of the entry of life-saving supplies – including desperately needed fuel – through Rafah and Kerem Shalom crossings.”
The evacuation order on Saturday told residents to go to the “humanitarian zone” of Al-Mawasi, on the coast northwest of Rafah.
That area has “extremely limited access to clean drinking water, latrines” and other basic services, according to Sylvain Groulx, Doctors Without Borders (MSF) emergency coordinator in Gaza.
The army late on Friday said rocket fire from Gaza hit Beersheba, Israel’s main southern city, for the first time since December. One civilian was wounded.
In New York, the UN General Assembly voted overwhelmingly to grant the Palestinians additional rights in the global body and backed their drive for full membership, vetoed by Washington at the Security Council.