Egyptian Foreign Minister Mohamed Kamel Amr said Cairo was seeking "clarification" concerning statements made by foreign officials. On Monday, Clinton said the violence in Egypt was shocking and served as a "systematic degradation of women."
Protesters have called for a mass rally on Friday to demand an apology for the attacks on women. Soldiers have beaten female protesters, dragged them by their hair, and in some cases, pulled off their clothing.
Photo Gallery: Protesters talk about political crisis
The military council said Tuesday that it regretted the attacks on women, and said it would take legal action against those responsible for the abuse.
Five days of clashes between security forces and protesters in Cairo's Tahrir Square have killed at least 14 people, as demonstrators call for an end to Egypt's military rule.
The military is overseeing a three-month parliamentary election process and has promised to hand power to an elected president by July.
Voters in nine Egyptian provinces began voting in runoff elections Wednesday. The voting is taking place in mostly rural areas to decide contests in which there was no absolute winner in elections held last week.
Demonstrators have accused the ruling military council of manipulating the country's transition process to retain permanent powers.
The party of Egypt's main Islamist group, the Muslim Brotherhood, and the ultra-conservative Islamist Al-Nur party dominated the first stage of voting for the lower house of parliament last month, which included Cairo.
Each stage includes a third of Egypt's provinces, with the final group set to vote in early January.
"Women protesters have been rounded up and subjected to horrific abuse. Journalists have been sexually assaulted. And now, women are being attacked, stripped, and beaten in the streets. This systematic degradation of Egyptian women dishonors the revolution, disgraces the state and its uniform, and is not worthy of a great people," Clinton stated.
"The reason for the protest is the picture and the video that was published by news services around the world, and it showed us to what extent the military council has no qualms about trampling on the women of Egypt and the girls of Egypt, and to beat them up and strip them. They have no problem doing that, so long as they get to stay in power, and cover up their crimes, and the regime remains in place, protecting Mubarak, and the previous regime, which has still not fallen,'' noted Islama Thabet, Egyptian female protester.
"Our demands to the military are - enough, they have proven that they failed during this last period. Not only were they unable to protect the country, they were unable even to protect women in the streets," said Salwa, Egyptian female protester.
Analysis: Said Sadek, Professor of Political Sociology at American University in Cairo, discusses Egypt's Islamist parties.
Some information for this report was provided by AP and AFP.