"Some 200 women have been arrested since the application of the anti-protest law," the "Woman against coup" group said in a report.
Egypt's anti-protest law makes it necessary for protest organizers to seek approval from the Interior Ministry before staging protests.
The group said that 35 female students from Al-Azhar University are among women detainees in Egyptian prisons.
According to the group, the highest number of women was registered on December 27 when 40 female supporters of Morsi were arrested.
The group said that six Al-Azhar students were slapped with one-year jail terms in January and six pro-Morsi women were sentenced to five years in prison.
"Female detainees are forced to totally undress inside police stations," the group alleged. "They are also beaten and placed in bad prison cells."
It went on to allege that female detainees are forced to undergo pregnancy and virginity tests in "a humiliating and inhumane manner and then placed with criminal prisoners".
The London-based Arab Organization for Human Rights said Wednesday that it had received complaints from the families of 12 female student detainees that their daughters were subject to beating, humiliation, and sexual harassment at the hands of officers and soldiers.
But an Interior Ministry official categorically denied the allegations.
"The claims are groundless and bare of truth," Assistant Interior Minister Ali al-Demerdash told AA.
He said that Egyptian prisons "follow international human rights standards".
"The claims about torture and violence inside Egyptian prisons are totally untrue," he said.