And it's calling for an immediate and impartial investigation.
The three Gazans were among over 400 people, who, earlier in the evening had fled their homes in Beit Lahia in northern Gaza and had been given refuge in the UNRWA school.
The three men, all from the same family, were killed as they left the school's toilet at 11:30 last evening when the school compound took a direct hit.
UNRWA says where it is found that international humanitarian law has been violated, those responsible must be held to account.
Under international law, installations such as schools, health centres and UNRWA facilities should be protected from attack.
UNRWA says well before the current fighting, it had given to the Israeli authorities the GPS co-ordinates of all its installations in Gaza, including the Asma Elementary School.
UNRWA says this tragic incident again illustrates the most urgent need for an end to the fighting. It also underlines the sad reality facing those fleeing the violence that unless there is a lasting ceasefire, there will remain pervasive risks to civilian lives in Gaza today.
This is Donn Bobb reporting for United Nations Radio.
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