Although Save the Children said it could not confirm the reports, the charity said the accounts by children were consistent and they were displaying signs of physical and emotional distress.
The allegations come from 200 children and 40 adults who have fled from Misrata, Ajdabiya and Ras Lanuf and are now in temporary camps in the rebel stronghold of Benghazi.
The families told the charity's staff that children as young as eight had been sexually assaulted, sometimes in front of their relatives.
In one reported case, mothers claimed a group of girls had been abducted, held hostage for four days and raped, and were unable to speak when they were released.
Michael Mahrt, Save the Children's child protection adviser, said: "The reports of sexual violence against children are unconfirmed, but they are consistent and were repeated across the four camps we visited.
"Children told us they have witnessed horrendous scenes. Some said they saw their fathers murdered and mothers raped. They described things happening to other children, but they may have actually happened to them and they are just too upset to talk about it – it's a typical coping mechanism used by children who have suffered such abuse."
Mahrt said some children were displaying signs of physical and emotional distress: being withdrawn, refusing to play and waking up crying in the night.
The charity, along with other agencies, is conducting a 13-day assessment of the situation. It called on "the international community to ensure that all parties respect children's right to be protected from violence and abuse".
The charity said it was increasing its child protection work in Benghazi, training social workers to provide youngsters with psycho-social support.
Further Information:
- MENA: State crackdown on pro-democracy demonstrations continues (20 April 2011)
- LIBYA: Schoolboy conscripts shot by Gaddafi forces for refusing to fight (18 April 2011)
- LIBYA: 'Gaddafi forces killed 10,000' (12 April 2011)
- More on children's rights in Libya