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As many as 21,000 children in Gaza are estimated to be trapped under the rubble, detained, buried in unmarked graves, or separated from their families, Save the Children said on Monday.
The British advocacy group said the latest waves of displacement caused by Israel's offensive in Rafah – where thousands of Palestinians were seeking refuge – have separated more children from their families.
In its newly published report, Save the Children said it was "nearly impossible to collect and verify information under the current conditions in Gaza".
"Save the Children estimates approximately 21,000 children are missing in Gaza," the report said.
"At least 17,000 children are believed to be unaccompanied and separated and approximately 4,000 children are likely missing under the rubble, with an unknown number also in mass graves."
An unknown number of children have been "forcibly disappeared" including some who were "detained and forcibly transferred out of Gaza", with their whereabouts remaining unknown.
More than 14,000 children have been killed in Gaza since the war broke out on October 7, according to the enclave's Health Ministry and Unicef.
Gaza's Education Ministry put the number of children killed at 15,000 earlier this month.
Save the Children's regional director for the Middle East, Jeremy Stoner, called for an independent investigation to be conducted and for those responsible to be held accountable.
“Families are tortured by the uncertainty of the whereabouts of their loved ones," he said. "No parent should have to dig through rubble or mass graves to try and find their child’s body.
"Gaza has become a graveyard for children, with thousands of others missing, their fates unknown."
At least 37,600 Palestinians have been killed since the war started following an attack by Hamas on southern Israel which killed more than 1,200 people. The report said 33 Israeli children have been killed during the conflict.
It added that about 250 Palestinian children are also missing from the occupied West Bank in the Israeli military detention system. Their families are unable to confirm their locations and well-being due to an increase in restrictions on visits since October.
Save the Children also called for a ceasefire.
"We desperately need a ceasefire to find and support the missing children who have survived and to prevent more families from being destroyed," Mr Stoner said.
However, both Israel and Hamas have been moving further from a US-backed ceasefire proposal. On Sunday, Israeli Prime Minister Benjamin Netanyahu said he would back only a partial truce to return the hostages, and that fighting would continue until Hamas was destroyed.
