"We broke the barrier of fear, we delivered a message to the military that we are not scared," Milad Daniel, whose brother Mina was killed in a military crackdown on protesters in October, said after the ministry protest. "They have tanks and armored vehicles but we have God."
Divisions also boiled over in Tahrir Square, where scuffles broke out between the Muslim Brotherhood and secular protesters, who have been in competition over the gatherings this week to mark the one year anniversary of the protests that toppled Hosni Mubarak.
Many in the leftist and secular camp are suspicious of the Brotherhood, believing that now that it won domination of parliament it intends to strike a deal with the generals to give them continued power. The Brotherhood denies any deal.
The political differences have translated into a dispute over the very meaning of the anniversary. The Brotherhood has presented this week as a celebration of the revolution's successes. The secular groups say there is nothing to celebrate when so many demands of the revolution are left unachieved and killings of protesters have gone unpunished.
The fights erupted because of a giant stage the Brotherhood set up in the square since protests Wednesday, which some protesters complain has sought to dominate the gatherings there by blaring religious anthems and music. Others were angered a celebratory banner on the stage proclaiming, "Holiday of the Revolution."
Arguments over the music and banner turned to pushing and shoving, then fistfights and bottles and rocks thrown back and forth, witnesses said. When Brotherhood supporters formed a human chain in front of the state, protesters raised their shoes in the air at them in a show of contempt, chanting, "out, out, out," and "dogs of the military council."
The day's protests, which included mass rallies in other Egyptian cities, commemorated the first anniversary of the "Friday of Rage," one of the bloodiest days of the 18-day wave of protests a year ago that ousted Mubarak.
In last year's "Friday of Rage," Mubarak's security forces fired on protesters marching toward Tahrir from around the capital, killing and wounding hundreds. Protesters battled back for hours until Mubarak's widely hated police forces collapsed and withdrew from the streets.
A year later, protesters' focus is now on demands that the military, which has ruled since Mubarak's Feb. 11 ouster, leave power.
But here too, Islamists and leftist, secular-leaning "revolutionary" protesters are divided. The revolutionaries want the generals out immediately. The Brotherhood, which is now the most powerful bloc in parliament with just under half the seats, is willing to wait for the military's promises to step aside by the end of June.
The leftists and secular groups accuse the military of being as dictatorial as Mubarak and of intending to preserve their power even after handing over their authority to civilians. Regardless of the timetable, there is widespread resentment that little has been done to dismantle Mubarak's regime and prosecute security officers for the deaths of hundreds of protesters during and after the anti-Mubarak uprising.
Amid the crowds in Tahrir, a Muslim cleric delivered a boisterous Friday sermon, proclaiming that the protesters, not the military, have the right to determine the country's course.
"Our right is to dictate the decisions of the revolution," said the cleric, Muzhar Shahine, speaking from the "revolutionaries" stage, as the crowd cheered and cried, "God is great."
He gave a litany of the unrealized changes sought by the revolution.
"A year later, has State Security really been dissolved," he said, referring to Mubarak's feared internal security force that was the backbone of his police state. "Has our land been freed?" He said state media, a key mouthpiece for Mubarak and now the military, must be purged, a constitution must be written that is "shared by all political parties and that gives rights for all of Egypt's children," and Christians must be given the same rights as Muslims.
Rallies of thousands of protesters moved from main mosques all around Cairo to Tahrir, chanting "we want civilian, not military." Some young men had shaved the words "down with military rule" in their hair cuts.
"This is a day of mourning, not celebration," said Abdel-Hady el-Ninny, the father of a slain protester, Alaa Abdel-Hady. He and his family carried large posters of his son around Tahrir.
Friday's protests come two days after hundreds of thousands packed into Tahrir to mark the Jan. 25 start of the uprising against Mubarak. That rally, too, was marked by similar divisions.
There were increasing calls among many protesters for presidential elections to be moved up to April to select a civilian for the military to give its powers as head of state. Under the military's timetable, presidential elections would be held by late June after a new constitution is written, and after the election it would step down.
A youth umbrella group of liberal political forces and activists named "Our Egypt" or "Masrana" issued a statement Thursday calling for a presidential vote before the constitution, a demand repeated in a large banner in Tahrir on Friday.
Supporters of the idea says the constitution should be written under the rule of a civilian president, because the military may try to force provisions that give it a political say or prevent civilian oversight.