"The death toll is now between 90 to 100 and there are dozens more wounded. Three Israeli rockets hit the school that was housing displaced Palestinians," agency spokesman Mahmud Bassal told AFP. Gaza's government media office said there were "more than 100 martyrs" in the strike.
The Israeli military said it struck a Hamas "command and control centre" that was "embedded" in Al-Tabi'een school in the Daraj neighbourhood.
"Numerous steps were taken to mitigate the risk of harming civilians, including the use of precise munitions, aerial surveillance, and intelligence information," a statement said.
The Islamic Jihad Palestinian military group said that the strike took place "during the dawn prayer".
Ismail Al-Thawabta, director general of the Gaza government media office, told AFP that the strike "resulted in more than 100 martyrs and dozens of injuries, most of which are in severe and critical condition".
Gaza government media sources said the school was housing about 250 women and children, about half of them women and children.