The head of the UN agency for Palestinian refugees, which runs the school, described the strike as horrific.
An Israeli air strike on a UN school packed with displaced Palestinians in central Gaza has reportedly killed at least 45 people.
Local journalists told the BBC that a warplane fired two missiles at classrooms on the top floor of the school in the urban Nuseirat refugee camp this morning.
Israel's military said it conducted a precise strike on a Hamas compound in the school and killed many of the 20 to 30 fighters it believed were inside.
However, Gaza's Hamas-run Government Media Office denied the claim and accused Israel of carrying out a horrific massacre.
The head of the UN agency for Palestinian refugees, which runs the school, also described the incident as horrific and said the claim that armed groups might have been inside a shelter was shocking, but could not be confirmed.
The al-Aqsa Martyrs' Hospital has been overwhelmed since the Israeli military began a new ground operation against Hamas in central Gaza this week.
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