Rights campaigners say more than 20,000 Egyptians are in detention in police stations and prisons and allegations are mounting they are enduring hard beatings.
Some young male detainees say they are being routinely sexually assaulted in a bid to break them psychologically.
Both the interior ministry and public prosecutor have denied any abuses, though there has been no response from authorities to individual allegations.
Human rights groups are mounting a vocal and public campaign to publicize the abuse allegations, including a recent appearance by several alleged victims in Cairo’s Press Syndicate headquarters.
When the parents and family members of 19-year-old student Fadhy Samir Zakher visited police stations in Cairo frantically trying to locate him, they feared the worst.
For 39 days he was held in detention after he had been arrested during a demonstration against Egypt’s new military rulers. He was released last week
But his parents’ were horrified to learn their son said he not only was regularly and viciously beaten during the first few days of his incarceration, but he said he also was sexually assaulted during interrogations.
"They made me and other 10 young men who had been arrested to strip naked when we arrived at Cairo’s Abdeen Police Station; they blindfolded the boys with their own underwear and there were a lot of beatings," said Zakher. "The police used sticks and their fists, and they also kicked the detainees repeatedly."
Zakher said they accused him of being a member of the outlawed Muslim Brotherhood, which has been declared a terrorist organization, but he said he kept trying to explain to them that he could not be as he is a Coptic Christian.
Zakher said that later during three interrogations by state security officers he was again blindfolded and beaten before each question. The main interrogator ordered one of the officers to sexually assault him, he said.
Few of those who have allegedly been sexually assaulted in detention, whether male or female, seek professional counseling after their release because of feelings of shame and cultural stigmas, said psychiatrist Ahmed Abdellah.
"Some friends told me about some girls especially, and I said, 'I am OK, I am ready to receive them," he said. "But it [is] very hard for the families."
Sixteen Egyptian human rights organizations have called for an independent investigation into widespread allegations.
In a written statement to the U.N. Human Rights Council, Amnesty International accused Egyptian security forces of committing gross human rights violations since last July when the army ousted Egyptian president Mohamed Morsi.
Amnesty accuses the army and police of using excessive force to disperse protests and arresting political opponents, journalists and NGO workers.