The subject was raised by the London-based rights group's chief, Salil Shetty, at a meeting in the Egyptian capital with the head of military intelligence, General Abdel Fattah al-Sisi.
"He said virginity tests were carried out to protect the army against possible allegations of rape, and added that the army does not intend to detain women again," an Amnesty statement said.
Sisi is a member of the Supreme Council of the Armed Forces (SCAF), to which president Hosni Mubarak transferred power when he was ousted on February 11.
The general is the first identified Egyptian military official to acknowledge that forced virginity tests have taken place.
On May 31, Amnesty called on the authorities in Egypt to bring to justice those responsible for forced virginity tests on female protesters, slamming it as "nothing less than torture."
Amnesty's statement came after an apparent admission by an unnamed army general to CNN that women detained on March 9 in Cairo's Tahrir Square had been subjected to virginity tests.
A senior military official on May 31 denied to AFP reports that the army had conducted such tests, saying "these allegations are baseless."
Amnesty opposes forced virginity tests under any circumstances.
"Sisi said people alleging abuses should complain to the military prosecutor and could also post their complaints on the SCAF Facebook page," the Amnesty statement said.