A report by the organisation suggests men, women and children are being abused "to eliminate public protest".
Many are subjected to virginity tests, rape and gang rape after arrest.
Egypt's Interior Ministry said it would not comment until it had studied the report.
The study notes a surge in sexual violence after the Egyptian military takeover in July 2013.
The perpetrators are rarely held to account and the impunity points to a "cynical political strategy aimed at silencing all opposition".
Police, intelligence officers and members of the military are guilty of targeting male and female detainees, according to the report.
Among the victims are student demonstrators, human rights activists, gay people and children.
Student's ordeal
I saw an officer who was grabbing a young woman by the breasts and I said to him: "If you want to arrest her, then arrest her, but you have no right to touch her breasts."
He grabbed me exactly as he had her, before calling two other police officers to come and hold me. They beat me, insulted me.
In the van they insulted me and beat me so much that I could no longer stand up. Two soldiers started to sexually assault me.
The officer from the start got into the van and said to me: "Come here I'm going to show you if I'm a man." He sexually assaulted me, the soldiers laughed, and then he raped me completely. I was paralysed, I started to vomit blood.
My life is ruined. I'm afraid of my son, my husband and even my father.
The authors said they did not have evidence that commanders were giving the orders, but the scale of the violence - and the impunity - suggested there was a political strategy.
They claim that victims who file complaints are systematically obstructed by the justice system, and face threats and reprisals by police officers and prison guards.
Sexual violence has long been a problem within the general population in Egypt, with assaults dramatically increasing in the years since Hosni Mubarak was removed from power.
Last year, President Abdul Fattah al-Sisi ordered police to launch a crackdown amid growing public anger.
He said sexual assaults, were "an unacceptable form of conduct" and called for citizens to "reinstate moral values in society".
Egyptian security forces are using sexual violence against detainees on a massive scale, according to the International Federation for Human Rights.