Israel said it carried out two of the strikes that the civil defence agency said also left dozens more wounded.
According to an updated toll, 25 people died at the UN-run Al-Razi School in the Nuseirat refugee camp in central Gaza, an agency director, Mohammed al-Mughair told AFP.
At least 18 people were killed and 25 wounded at Al-Mawasi near the southern city of Khan Yunis. Five people were killed in a strike on people stood near a roundabout at Beit Lahia in northern Gaza, according to the official.
The Israeli military said "terrorists" used the Nuseirat school to launch attacks on its troops and that a Hamas "company commander" was the target of the attack at the Al-Attar district of Al-Mawasi.
At least seven schools, many of them managed by the United Nations when in operation, have now been the targets of Israeli strikes in 10 days. Most of Gaza's schools have become shelters for thousands of people displaced since the war started on October 7.
Al-Mawasi is where more than 90 people were killed in a huge Israeli bombing raid on Saturday aimed at the Hamas military chief Mohammed Deif and one of his deputies.
Tens of thousands of people had sought refuge in a tent city in Al-Mawasi after Israel declared it a safe zone from military offensives in Gaza.
Mohammed Zaqut, Gaza's director general of hospitals, told AFP that Israeli forces "carry out massacres in the Al-Mawasi area, which it claims is safe, knowing that any bombardment, even with a small missile, will kill dozens of people and cause many injuries because these are densely populated areas."
The Israeli military said it was "looking into the reports stating that several civilians were injured as a result of the (Khan Yunis) strike. The details are under review."
The Israeli military said after the latest strikes that "numerous steps were taken in order to mitigate the risk of harming civilians, including the use of aerial surveillance, precise munitions, and additional intelligence."
It said Hamas "systematically violates international law, exploiting civilian structures and population as human shields for its terror attacks".
The war began with Hamas's unprecedented October 7 attack on Israel which resulted in the deaths of 1,195 people, mostly civilians, according to an AFP tally based on Israeli figures.
Israel's retaliatory campaign has killed at least 38,713 people, also mostly civilians, according to figures from Hamas-run Gaza's health ministry.
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