The unidentified protester was among many women arrested in Cairo's Tahrir Square March 9 and subjected to the abuse, Bikya Masr reports.
The Egyptian Initiative for Personal Rights, the Nadeem Center for the Rehabilitation of Victims of Violence and Torture and the Hisham Mubarak Law Center filed the complaint in an administrative court Tuesday.
They say the woman was tried in a military court without being told of the charges and "was exposed to the worst kinds of humiliation, torture and violation to the sanctity of her body to the extent of inspecting her virginity within view and earshot of army prison workers."
A general, speaking anonymously, told CNN women arrested March 9 were subjected to the tests despite official denials.
He asserted they "were not like your daughter or mine. These were girls who had camped out in tents with male protesters. … We didn't want them to say we had sexually assaulted or raped them, so we wanted to prove that they weren't virgins in the first place."
"This admission is an utterly perverse justification of a degrading form of abuse," said Amnesty International.