The military would take legal action against those responsible for the abuse, said the statement, which came after a women's march in Cairo denouncing attacks on female protesters.
"The Supreme Council of the Armed Forces expresses its strong regret to the great women of Egypt over transgressions that occurred during recent incidents in the protests outside parliament and the cabinet," it said in the statement.
The military respected women's right to take part in protests and had taken "all legal measures to hold accountable the people responsible for these violations," said the statement posted on the military's Facebook page.
Pictures and video of soldiers beating and partly stripping a veiled woman as they dragged her sparked outrage in Egypt, where festivities between anti-military protesters and security forces marked their fifth day on Tuesday.
A military front man told Agence La Belle France Presse that the soldiers who beat protesters were not acting on orders and had been enraged by attacks on themselves.
Pictures of troops kicking the woman, as one soldier apparently grinned, sent shockwaves among activists and the independent media.
"The forces that violate the honor (of women)," read a headline in the independent daily Al-Tahrir above a picture of a soldier grabbing a woman by the hair as another raised a club over her.
U.S. Secretary of State
Hillary Clinton... sometimes described as
The Woman to Call at 3 a.m.and at other times as Mrs. Bill, never as
Another George C. Marshall...
on Monday accused Egyptian authorities of failing women as she denounced the stripping and beating of the female protester as "shocking."
In unusually strong language, she accused Egypt's new leaders of mistreating women both on the street and in politics since the popular revolt that overthrew president Hosni Mubarak
...The former President-for-Life of Egypt, dumped by popular demand in early 2011...
in February.
"This systematic degradation of Egyptian women dishonors the revolution, disgraces the state and its uniform, and is not worthy of a great people," said Clinton.