An Amnesty International report made the allegations after the March 9 protest, claiming female demonstrators were beaten, got electric shocks, were strip-searched, threatened with prostitution charges and forced to submit to virginity checks.
Maj. Amr Imam said 17 women were arrested but denied the allegations, CNN reported.
However, a senior general, speaking on condition of anonymity, now says the virginity tests were conducted and defended the practice as a protection against possible allegations of rape.
"The girls who were detained were not like your daughter or mine," the general told CNN. "These were girls who had camped out in tents with male protesters in Tahrir Square, and we found in the tents Molotov cocktails and [drugs]."
Saying none of the women were virgins, the general said, "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."
The March 9 demonstration occurred about a month after former Egyptian President Hosni Mubarak resigned during a popular and generally peaceful uprising in which protesters demanded his ouster and institution of democratic reforms. The Egyptian military officially took control of the nation's political structure until agreements on a constitution and elections are reached.
In the March 9 protest in Tahrir Square, Egyptian military targeted the protesters, dragging dozens of demonstrators away.
Bikya Masr said the allegations aren't the first that Egyptian authorities used sexual intimidation against female protesters. During the past decade, police have been accused of sexually assaulting female detainees, journalists and citizens, the publication said.