The ministry said the strike hit a shelter for displaced people in Al-Tabi'een School in Gaza City's Daraj district.
The Israeli army said it had "eliminated" in Gaza City a suspect in a May 2002 bombing which wounded 10 civilians in the Israeli city of Beersheba.
The military said it had also struck dozens of Hamas targets in the "combat zone" in the northern towns of Jabalia and Beit Lahia.
It said "troops operated to eliminate terrorists in aerial strikes and close-quarters encounters" at the former Al-Harthani School in Beit Lahia.
"During the operation, Hamas terrorists fired anti-tank missiles from the Indonesian Hospital at the troops," the army claimed.
Militant group Hamas condemned the "criminal military operation in northern Gaza".
Earlier on Wednesday, a senior Hamas official hailed the truce in Lebanon, adding that the group was ready to reach a ceasefire in Gaza.
A ceasefire between Israel and Hezbollah took effect before dawn, ending more than a year of hostilities and two months of full-scale war.
Gaza's civil defence agency said it had only one working rescue vehicle in the whole of the territory due to fuel shortages.
The Gaza war began with Hamas's unprecedented attack on Israel on October 7 last year, which resulted in the deaths of 1,207 people, most of them civilians, according to an AFP tally of Israeli official figures.
Israel's retaliatory campaign has killed 44,282 people in Gaza, according to figures from the health ministry that the United Nations considers reliable.
Lebanon PM says army to reinforce south after ceasefire
Beirut, Lebanon (AFP) Nov 27, 2024 -
Lebanese Prime Minister Najib Mikati said the army would reinforce the country's south while urging Israel to withdraw and respect a ceasefire that came into force on Wednesday.
The deal that halted 13 months of conflict between Israel and Lebanon's Hezbollah movement is largely based on the implementation of UN Resolution 1701, which ended their last war in 2006.
It stated that Lebanese troops and UN peacekeepers should be the only forces in the south, where Hezbollah exerts control, and also calls for Israeli troops to withdraw from Lebanese territory.
Mikati said his cabinet had decided to "strengthen the deployment of the army and security forces in the South Litani region", in their first meeting following the ceasefire.
"I demand that the Israeli enemy abide by the ceasefire deal and withdraw" from Lebanese territory, he said.
"I hope this will be a new page for Lebanon, I hope the coming days will lead to the election of a president."
Bickering between Hezbollah and its political adversaries has left Lebanon without a head of state for more than two years.
Earlier, Lebanon's powerful parliament speaker Nabih Berri called on those displaced by war with to return home as the ceasefire took hold, also calling for the quick election of a president who can unite the country.
"I invite you to return to your homes... return to your land," said Berri, despite warnings to the contrary from Lebanon and Israel's militaries.
Berri heads the Amal movement and has led ceasefire talks on behalf of ally Hezbollah.
After nearly a year of limited cross-border fire initiated by Hezbollah over the Gaza war, Israel ramped up its aerial bombing of Lebanon on September 23, mainly hitting Hezbollah strongholds.
It later sent ground troops across the southern border.
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