The hundreds of people detained Friday will be held for 15 days pending investigation, the official said. They face charges of attacking military troops, being present in a restricted military area despite warnings and disrupting public order. The detainees are likely to face military trials.
At least 26 women are also being held, the official said speaking on condition of anonymity because he was not authorized to speak to the media.
The official said at least two of the detainees are also facing charges of killing one soldier during the clashes.
The military council had warned the demonstrators before the march that deadly force would be used against them if they approached the ministry. One warned protesters they would be approaching the "lion's den."
Over 300 people were injured by tear gas, rocks, and live fire. Security officials said 140 soldiers were injured.
An overnight curfew was imposed following the clashes. A military official said a curfew will be in place again Saturday from 11 p.m. to 6 a.m. around the ministry.
He was also speaking on condition of anonymity in accordance with military regulations.
Maj. Gen. Mukhtar al-Mullah, a member of the military council, warned late Friday that those involved in or instigating violence would be arrested.
On Saturday, the head of the military council, Field Marshal Hussein Tantawi visited the injured troops and inspected the area of the clashes. State TV showed footage of the funeral of the slain soldier.
Lawyer Ragia Omran said the roundup is one of the largest mass arrests following protests during the country's troubled transition. She said the number of detainees could still rise.
The tension in the area started earlier this week when protesters, predominantly supporters of an ultraconservative presidential candidate who was barred from running in the presidential election, held a sit-in outside the ministry starting last Saturday.
Deadly clashes broke out when apparent supporters of the military rulers attacked the crowd Wednesday.
Nine people were killed in those clashes, drawing in anti-military protesters from different revolutionary groups who called for the Friday rally demanding the ruling generals stick to their pledges to step down after the elections.
Political groups criticized the swift prosecution of protesters after Friday's demo, saying no such action was taken after nine civilians were killed in the earlier clashes. The powerful Muslim Brotherhood said it was "astonishing and surprising."
Anger at the ruling military council has risen across the political spectrum. The generals are accused of steering a messy transition, using oppressive measures and maneuvering to maintain a degree of power even after the presidential election and handover of authority.
These recent protests have been spearheaded by Islamists rather than members of the country's left- and liberal-leaning movements who drove last year's uprising that toppled Mubarak.
The Islamists joined in after the disqualification of two heavyweight Islamists, Hazem Abu Ismail and Muslim Brotherhood chief strategist Khairat el-Shater. The Brotherhood has been frustrated that its domination of parliament - where it holds nearly half the seats - has not translated into political power.
The military still has the support of many Egyptians who are critical of the disruptions caused by street protests or who believe the military provides strong government.
The generals renewed this week their pledge to hand over power as soon as a president is elected.
Intellpuke: You can read this article by Associated Press writer Sarah El Deeb, reporting from Cairo, Egypt, in context here: www.guardian.co.uk/world/feedarticle/10228801