Mar 30, 2007
They were shot by soldiers, run over by armoured vehicles or crushed by stampeding animals last month.
The aid group said it had not found physical evidence of the alleged deaths in Karamoja, but had consistent reports after interviewing some 200 people.
The army denied the allegations, saying only adults were killed in the raids.
The BBC's Sarah Grainger in Uganda says there has been an increase in violence in Karamoja since the army began its disarmament programme in May last year.
"I saw many children killed, including my own son," one woman in Kaputh village near Kothido town told the BBC.
"He was with the livestock, trying to untie them so they could escape the firing. But he got crushed by the animals as they tried to run away."
Other villagers said the raid began at 0800 on 12 February.
A village elder greeted the army forces thinking they were carrying out a disarmament exercise, but was shot dead.
"I ran away like many people and when I came back both of my young sons were missing. Up till now I cannot find them so I think they were killed," another man said.
Army spokesman in Karamoja Lieutenant Henry Obbo said a five-day disarmament exercise had begun in the area on 10 February.
But when some warriors resisted the operation they opened fire on the army.
He said 52 warriors and four soldiers were killed in the incident, but no children were involved.
Save the Children has called for an independent investigation into the events at Kaputh.
"Reports of children being killed in indiscriminate, illegal and inhumane ways is absolutely devastating. Such allegations must be fully investigated and those involved brought to account," Save the Children's Valter Tinderholt said, Reuters news agency reports.