In a statement, it said Iraqi and U.S. soldiers were led to the Al-Hanan orphanage on June 10 by members of a neighborhood council and immediately took the children to hospital.
It said the boys, aged 3 to 15 years old, were found naked in a darkened room without any windows, and that many of them were tied to their beds and were too weak too stand once released.
"In a nearby locked room, the soldiers discovered a room full of food and clothing that could have been used to aid the children," it said.
Iraqi Prime Minister Nuri al-Maliki has vowed to investigate and punish those responsible.
Two orphanage workers have since been arrested.
(Reuters, AFP, AP)