AFP could not independently verify the toll which, if confirmed, would be one of the largest from a single strike during 10 months of war between Israel and Palestinian militants since Hamas's October 7 attack.
The bombardment of Al-Tabieen religious school and mosque drew criticism from across the Middle East and beyond alongside calls for a ceasefire, after international mediators invited the warring sides to resume talks towards a long-sought truce and hostage-release deal.
Civil defence rescuers in the Hamas-ruled territory said three Israeli missiles hit the complex in Gaza City while people were performing dawn prayers. The military confirmed it had used "three precise munitions".
Mahmud Bassal, spokesman for the civil defence agency, said 11 children and six women were among the 93 who died at the school shelter, "and there are many unidentified body parts".
"They dropped a missile on them while they were just praying," said one woman, mourning over a dead child shrouded in a plastic body bag.
Israel's military said it had "precisely struck" Al-Tabieen, later adding that intelligence suggested "at least 19 Hamas and Islamic Jihad terrorists were eliminated".
Hamas denounced it as a "dangerous escalation", while the Palestinian group's Lebanese ally Hezbollah called it a "horrific massacre".
Iran, which backs both militant groups and had accused Israel of wanting to spread war in the Middle East following high-profile killings in Tehran and Beirut, condemned what it called a "barbaric attack".
"Those who were inside the mosque were all killed," said local resident Abu Wassim. "Even the floor above, where women and children were sleeping, was completely burned."
With nearly all of the Gaza Strip's 2.4 million people displaced at least once during the war, many have sought refuge in school buildings, which have been hit at least 14 times since July 6, according to an AFP tally.
- 'Intolerable' toll -
Israel has made similar accusations of armed activities after strikes on school shelters, while Hamas has denied using civilian facilities for military aims.
US National Security Council spokesman Sean Savett said Hamas has been operating out of schools, "but we have also said repeatedly and consistently that Israel must take measures to minimise civilian harm".
Jordan's foreign ministry said the timing was an indication of Israel's efforts to "obstruct and thwart" the latest mediation effort.
One of the mediators, Qatar, called for an "urgent international investigation", while Turkey claimed Israeli Prime Minister Benjamin Netanyahu wanted "to sabotage ceasefire negotiations".
Hamas's October 7 attack that sparked the war resulted in the deaths of 1,198 people, mostly civilians, according to an AFP tally based on Israeli official figures.
Palestinian militants seized 251 hostages, 111 of whom are still held in Gaza, including 39 the Israeli military says are dead.
Israel's retaliatory military campaign in Gaza has killed at least 39,790 people, according to Gaza's health ministry, which does not give details of civilian and militant deaths.
The European Union's foreign policy chief Josep Borrell said the school strike left him "horrified".
France said "Israel must respect international humanitarian law".
"For several weeks, school buildings have been repeatedly targeted, with an intolerable number of civilian victims," the French foreign ministry said.
- Measured response -
Netanyahu's office on Thursday said Israel would send negotiators "to conclude the details of implementing a deal", after the joint invitation from the United States, Egypt and Qatar. Hamas has yet to formally respond.
Hamas officials, some analysts and critics in Israel have said Netanyahu has sought to prolong the fighting for political gain.
Anti-government protesters rallied again on Saturday in Israel's commercial hub of Tel Aviv and in the northern city of Haifa to pressure their leaders to secure the release of the remaining hostages.
Savett, the US spokesman, said the Gaza City strike "underscores the urgency of a ceasefire and hostage deal".
The mediators invited the warring parties to resume talks on August 15, after intense diplomacy aimed at averting a region-wide conflagration in recent days.
The Gaza conflict has already drawn in Iran-aligned groups around the region, but fears of a broader war have surged following the killings of two senior militants, including Hamas's political leader.
Iran, Hamas, Hezbollah and others have vowed retaliation, although they have yet to take action.
Asked what his message was to Iran, US President Joe Biden responded: "Don't", as he walked out of Saturday evening mass in Delaware.
Hezbollah, which has traded near-daily fire with Israeli forces throughout the war, on Saturday said it had fired "squadrons of explosive-laden drones" at an army base in retaliation for the killing of a Hamas commander in south Lebanon on Friday.
The killing on July 31 of Hamas's Ismail Haniyeh during a visit to Tehran had sidelined truce talks. Iran and Hamas blamed Israel, which has not directly commented.
Iran's mission to the United Nations on Saturday said the Islamic republic has "the legitimate right to self-defence" after its sovereignty was "violated".
"However, we hope that our response will be timed and conducted in a manner not to the detriment of the potential ceasefire," it said.
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