There is a huge problem going on in Egypt, according to the thousands of democracy activists who continue to pour into Cairo’s Tahir Square. And the issue, despite its importance to the strength of Egypt’s democratic transition, is not getting much attention from the United States or the United Nations.

Hosni Mubarak and his hated internal security services may be gone but the vestiges of the old regime are still being used by the Egyptian military to retain order, prosecute demonstrators who fail to abide by curfew and instill a signal to the Egyptian people that a switch to political freedom is not going to come without some obstacles along the way. And if this Washington Post article is any indication of what the protesters are experiencing, the hallmarks of democracy could very well be in jeopardy.

Mona Seif may not be a household name in Egypt, akin to that of Nobel Prize laureate Mohamed ElBaradei or Arab League Chairman Amr Moussa, but that is not stopping her from investigating thousands of cases indicting members of the Egyptian military for abuse over the past month and a half.

Working as an associate in the Hisham Mubarak Law Center, Seif has unveiled a cache of documents, totaling 5,000 cases, where the military detained protesters on trumped up charges, hauled them away into overcrowded prisons and prosecuted them in military courts. Charges such as violating curfew, carrying a weapon and assaulting law enforcement personnel are frequently used by Egyptian soldiers to round up demonstrators continuing to protest against the slow pace of reforms, with some of those prosecutions resulting in multiyear prison sentences. Those unable to afford a decent lawyer, like the vast majority of Egyptians, are increasingly lost in a prosecutorial system without much hope of challenging the state.

In other words, “the military is governing according to decrees similar to those relied on by Mubarak.” For the tens of millions of Arab activists who are demanding better control over their own lives, cases such as these have the danger of halting momentum and showing Arab governments in similar situations that repressive tactics work to maintain their positions.

However disturbing these accounts are, the Egyptian people need not diminish their hopes for a new and more open political system. Indeed, the practices being used by the Egyptian military thus far appear to be more in line with molding the future of the democratic transition than hijacking it outright.

It is important to remember that the Egyptian military, especially under Mubarak, transformed itself into the most powerful institution in the entire country. Authoritarian politics proved to be quite beneficial to the generals, all of whom expanded their business contacts, collected billions of dollars in expenditures annually and earned millions more in profits from their private corporations.

In exchange for absolute loyalty to the Mubarak regime, the Egyptian military was awarded greater freedom of maneuver in the economic realm. The military’s patronage network, which it depends on for gaining new recruits and paying soldiers already in their ranks, rose to a level that was unheard of under Presidents Gamal Abdel Nasser and Anwar Sadat. Factories owned by the military produced products that had a high demand in society and farms operated by the generals grew and sold cheap bread for millions of Egyptians who were unable to purchase it at market prices.

With Mubarak gone, that economic advantage is in peril. The transfer of power to civilian leadership runs the risk of curtailing the perks that the Egyptian military has come to take for granted over the past three decades. Egypt’s new president may not be as supportive or sympathetic to the military’s business ventures.

Call it an excuse, but the abuses currently undertaken by the armed forces could simply be an attempt to ensure that calls for democracy do not get out of hand. Egyptians are tired of being marginalized politically, so it is understandable that so many are worried about the military undercutting civilian politics before the process even begins.

This month’s referendum established parliamentary and presidential elections starting in September. The Supreme Military Council may just be using its authority for the time being to defend its interests before the soldiers return to the barracks.

It isn’t exactly the most ethical practice that the military can implement. But it’s not necessarily the death of Egyptian democracy either.