AMY GOODMAN: The Egyptian government has apologized for a violent crackdown that left at least two protesters dead and dozens wounded. The violence broke out after thousands gathered in Cairo’s Tahrir Square to call for the prosecution of the former president, Hosni Mubarak, and other officials. Friday’s demonstration was the largest in Tahrir since Mubarak’s ouster two months ago. Soldiers later attacked a group of protesters who peacefully remained in the square overnight. Dozens of people were also arrested and may now face military trial. On Monday, Egyptian Prime Minister Essam Sharaf expressed the government’s “regret” for the violence and said he will seek a judicial probe.

The crackdown comes at a time many Egyptians are questioning the role of Egypt’s military in the post-Mubarak era. The ruling military council initially had wide popular support. But with repression continuing — and Mubarak loyalists still holding key positions — there are growing fears the military could be used to contain the revolution it once stood beside.

Democracy Now! correspondent Anjali Kamat is in Cairo covering the Egyptian uprising. She filed this report.

ANJALI KAMAT: “The army and the people are one hand.” This became one of the most popular chants of Egypt’s 18-day uprising that ousted former President Hosni Mubarak. It began when the army took over Cairo’s streets following the collapse of the security forces and grew even louder once Mubarak fell and the Supreme Council of the Armed Forces took control of Egypt’s transition to a civilian democracy.

But increasingly the army is beginning to lose some of its popularity. In recent weeks, protests across the city have raised slogans against Major General Mohamed Hussein Tantawi, the leader of the military. While Egyptians have traditionally held the armed forces in high esteem, many are now beginning to be frustrated with the slow pace of change and question Tantawi’s close ties to Mubarak.

KHALED FAHMY: I think that the gravest danger on this revolution is the Egyptian army. People, of course, have celebrated the position of the army, have embraced it, have recognized it for what it is. The army commands a huge amount of respect and affection. That is obviously true. But in my assessment, the army was forced to take the position it did, not because of any genuine belief in democracy, not because the high brass of the Egyptian army really genuinely believe in democracy — maybe some of them do — but I think mostly it’s because the army is very afraid that this revolutionary spirit would exceed the existing boundaries and reach the army itself.

ANJALI KAMAT: Khaled Fahmy is the chair of the History Department at the American University in Cairo. He explained that while certain figures from the Mubarak regime have been charged with corruption, they have been largely those associated with the former president’s son, Gamal Mubarak, the so-called new guard of businessmen-turned-politicians.

KHALED FAHMY: Only recently have we started hearing kinds of information that maybe some of the members of the old guard, who are friends of Tantawi — Zakaria Azmi, Ahmed Fathi Srour, Safwat El-Sherif. Those are people who made their names back in the '60s. It's interesting that the army is very slow in moving into that direction. What the army has been basically saying is, “We’re going to try big businessmen and the businessmen associated with Gamal Mubarak. So this is the old rivalry between the army and Gamal Mubarak that we’ve been hearing about for the past eight, nine years. The army is seizing the opportunity of the revolution to get rid of that wing once and for all. And — but beyond that, we have seen very little.

ANJALI KAMAT: On Friday, tens of thousands of people poured into Tahrir Square calling for Mubarak and his family to be prosecuted and accusing the military of colluding with Mubarak. They were emboldened by the presence of some two dozen military officers, who said they were fed up with the corruption within the military.

FIRST LIEUTENANT: [translated] We believe the Supreme Council of the Armed Forces is colluding with the old regime. We see no serious steps toward bringing corrupt officials to justice.

ANJALI KAMAT: But the protest was brutally crushed by the army, who stormed into the square along with riot police early Saturday morning to disperse the peaceful protesters.

KHALED FAHMY: The army is misbehaving in a number of ways. If we give it the benefit of the doubt, we say, at best, that they are ill-equipped, they don’t have experience running a country as complicated and sophisticated as Egypt, with as many problems as those of Egypt, and at worst, that the army is actually continuing the same old politics of the Mubarak regime, that in that, in a true sense, that the Mubarak regime has not collapsed, only its civilian wing has. But the military wing, which was, you know, the core of the army — of the regime, has not effectively collapsed yet. And the last thing that these generals would like to see is, let’s say, for a civilian minister of defense or for civilian oversight over the military budget or, let alone, of revolutionary demands for accountability and justice and transparency to be applied to the army itself.

ANJALI KAMAT: At least two people were killed in the violence this weekend, and the army arrested 42 others, who will receive military trials. But this is not the first time the military has cracked down on peaceful protesters or resorted to some of the same tactics as Mubarak’s hated security apparatus. Heba Morayef of Human Rights Watch has been closely following this issue.

HEBA MORAYEF: The military was deployed on the streets of Egypt’s major cities on January 29th. Throughout the period of Tahrir, we received reports and documented cases of protesters who were arbitrarily arrested and detained by the military, either in the vicinity of Tahrir Square or taken to military camps. And all of the detentions were in fact enforced disappearances. The military would detain people without allowing them any communication to their families or lawyers, and the military would not make public the detention of the people they took in. The detentions ranged from 12 or 14 hours to, in the longest case, to 18 days.

And then, from February 11th onwards, after the Tahrir protest, the big Tahrir protest, ended, there were a number of occasions when the military moved in to clear the square of protesters. The evening of February 25th, March 6th and March 9th were the biggest roundups. And on those occasions, again the military used force and beat protesters, just in the process of clearing the square. It arrested a number of peaceful protesters and beat and tortured dozens of them at the Egyptian Museum and at other places of detention. And then it brought them before military tribunals, and over — and hundreds of them were then sentenced to — by military courts to sentences ranging from one year to five years.

ANJALI KAMAT: Salwa al-Husseini is a 20-year-old from a small town in the Delta who’s been an active part of the protests in Tahrir since the beginning. She was an enthusiastic supporter of the Egyptian army until a month ago. On March 9th, Salwa was among dozens of peaceful protesters who were detained by the military after their sit-in at Tahrir Square was forcibly cleared. She says the 18 women who were arrested were strip-searched. Those who were unmarried were subjected to what the military called a “virginity test” and threatened with prostitution charges.

SALWA AL-HUSSEINI: [translated] I was terrified. I was scared, because a man was examining me. No one has the right, not even a doctor, to do that without our consent. Why did they do this to us? We weren’t doing anything wrong. We were defending our country.

ANJALI KAMAT: Aly Sobhy is a 28-year-old actor from Cairo. He was also detained and tortured on March 9th.

ALY SOBHY: [translated] While the army was dispersing the sit-in at Tahrir, I was on the phone with lawyers, journalists and human rights workers, relaying the names of those being detained. As I was doing that, a soldier arrested me, confiscated my phone, and took me inside the museum. There, an officer charged into my chest and knocked me down. Then the beatings began, with sticks and electric shocks. My hair used to be long. They tied my hair to a pole and beat me on my back with an electric cord. They filmed us with knives and Molotov cocktails in front of us and showed this on television. In the morning, they took us to the general military prison, and that night prosecutors interrogated us and told us we were accused of being thugs, possessing lethal weapons, explosives, and defying the curfew.

ANJALI KAMAT: The army has accused many of those they arrested of being thugs or baltaguia, who the army blames for continued instability across Egypt.

HEBA MORAYEF: There are legitimate concerns about an increase in criminal activity out on the streets. What the army has done, however, is to present its mass arrests and its reliance on military tribunals as part of their attempt to clamp down on this criminal activity, and they’ve ascribed all of this to the existence of thugs, baltaguia, which has become the military’s new favorite word. They were being accused of trying to disrupt public order, trying to slow down the path of progress that the military set out. So there’s very much this perception that anyone who stands in the way of the plan set up by the military could be considered a thug.

ANJALI KAMAT: Hundreds and possibly thousands of civilians remain in detention today after being sentenced by military tribunals over the past two months.

HEBA MORAYEF: Their sentences haven’t been ratified yet, so there is still a possibility that they may not be ratified and that there may be an order to reduce them. I think this is where the role of civil society becomes extremely important, because all of these people need to be released immediately under international law. None of them should have been brought before military tribunals.

ANJALI KAMAT: But thus far, abuses by the military have received little attention in Egyptian media.

HEBA MORAYEF: We know from journalists at some of the independent newspapers, who have come to press conferences, who have spoken to victims of torture, that they’ve tried to write about this, that they’ve tried to report on the cases, and that this has been blocked. We know that the military — criticizing the military is one of the red lines for the media and that last week newspapers and some lawyers received letters from the military saying that any — any publication of information about the military itself needs to receive prior authorization from the military.

ANJALI KAMAT: One blogger who openly criticized the military is now facing a military tribunal for his comments on Facebook and on his blog. Maikel Nabil was arrested on March 28th for insulting the military. His friend Sahar Maher explained the charges against him.

SAHAR MAHER: [translated] Maikel was charged with insulting the military establishment, publishing lies about it, and threatening public security. They were most concerned about his last blog post, entitled “The Army and the People Are Not One.” This was the main source of the accusations. Maikel saw that the army had committed violations, tortured people, beat people in Tahrir, and detained protesters without clear reason. Maikel was outspoken in the past, so the military already had him on their radar. He had previously created a Facebook page called “No to Forced Conscription.” He was once arrested on February 28th, and another time before that, for refusing to join the army as a conscientious objector.

ANJALI KAMAT: Maikel Nabil’s family and friends are outraged that he’s being tried in a military tribunal simply for expressing his point of view.

SAHAR MAHER: [translated] Nobody should be subjected to a military trial for expressing their opinion. We’ve just had a revolution. What may have been acceptable before the revolution should not be acceptable anymore. In the new Egypt we are building, people should not be tried and imprisoned for their opinions. And on top of that, this was a military trial. That didn’t used to happen before.

ANJALI KAMAT: A month after her ordeal with the military, Salwa al-Husseini hasn’t got any satisfactory answers from the military. She wonders why she and so many others have been abused by the very institution claiming to protect the revolution.

SALWA AL-HUSSEINI: [translated] To the army, the Supreme Military Council and Mubarak, Egypt is just a business, nothing more. This country is not the army or the government; it’s the people.

ANJALI KAMAT: As popular dissatisfaction with the military grows, many are beginning to question how it can guide a transition to a civilian democracy without compromising its own powers.

KHALED FAHMY: The quicker the army gets out of the picture, the better it is for its own cohesion and for the revolution itself. They know that this is dangerous. They know that — dangerous for itself. They know that getting out of the picture might mean true civilian control over the army itself. And I think this is exactly the kind of negotiation that they are trying to find — to chart now. In other words, they want out, but they want out in a way that would preserve their privileges — economic and political and military — and some kind of an overall blanket possible amnesty for abuses and corruption that are endemic within the army itself. That’s very tricky, and that is exactly where the danger comes, especially when we think about the connection with the U.S. military, because the U.S. wants the Egyptian army, and the U.S. doesn’t want true transparency to spread to the army, because that will implicate many American businesses and politicians and probably also generals.

ANJALI KAMAT: The recipient of $1.3 billion in U.S. aid last year, Egypt’s military has a very close relationship with the United States. Professor Fahmy warns that this alliance could prove fateful for the future of the Egyptian revolution.

KHALED FAHMY: The possibility of a counter-revolution, if it is there, it’s actually not from the remnants of the NDP, the National Democratic Party, as people fear, and it’s not definitely from the Islamists taking over. It would be from the Egyptian army colluding either with the Muslim Brotherhood — and that is possible — but more likely, colluding with the U.S. Army and/or Israel to try and limit the extent of this revolution and maintain some kind of a — you know, stop it in its tracks, to some degree, and even roll back some of the — some of the gains of the revolution.

ANJALI KAMAT: For Democracy Now!, I’m Anjali Kamat in Cairo, Egypt.

AMY GOODMAN: Special thanks to Ziyad Hawwas. And an update on the case of Maikel Nabil, the Egyptian blogger who was arrested for criticizing the military: on Monday, Nabil was sentenced by a military court to three years in prison.