Egyptians headed to the polls this week not knowing who will emerge victorious at the ballot box. Gone are the grim certainties that once defined Egyptian political life. But while this first post-revolution presidential election is competitive, it is not fully free and fair.

This is not to suggest that the country’s interim military rulers will engage in massive vote-rigging and fraud. In fact, the ultimate outcome of this presidential contest cannot be dictated by the Supreme Council of the Armed Forces (SCAF). However, SCAF continues to exercise ultimate control over state institutions in biased fashion and in furtherance of political goals. And the climate of selective repression continues even as boisterous political debate echoes throughout the country.

While bearing in mind the shortcomings of the current process, it is important to note that a boycott of the election would have been ineffective and counterproductive. There was no real popular movement to mobilize a boycott, and no real chance for achieving a critical mass of boycotters that could erode the legitimacy of the election. Based on projections of a fragmented first round of voting where competitors will be divided by small margins, a boycott, even if miniscule, would have increased the prospects for an adverse electoral outcome. There are actual substantive differences among the candidates despite the lackluster set of choices, and certain vote results could exacerbate the country’s already polarized politics and undermined the possibilities for creating an open and pluralistic political culture.

But while electoral boycotts would have been ill-advised, it is equally important to note the limitations of the current process. Despite the orderly scenes of excited voters, the absence of organized violence, and the fierce political debates that have gripped Egyptians, the manifest flaws of this election should serve as a reminder of the challenges that remain before Egypt’s emerging political order can be described as a fully free and fair democracy.

The bulk of the blame for this state of affairs inevitably falls upon SCAF and the largely unreconstructed state bureaucracy that it now leads. While the January 25 uprising managed to topple former President Hosni Mubarak and the inner core of his regime, the institutional backbone of that regime remains intact. SCAF’s assumption of outsized power was aided by the fragmentation of the Egyptian political class and its inability to unify behind a core set of revolutionary demands. This fragmentation–willfully exploited by SCAF–enhanced SCAF’s authority and allowed it to triangulate between the country’s polarized and fractious political factions. So although Egypt’s military leaders cannot dictate political outcomes, they have shaped the political environment and managed the process of competition.

In these tasks, state media has been SCAF’s most effective tool. It remains a key outlet for the dissemination of news and opinions and is still the primary source of information for many Egyptians despite the rise and proliferation of domestic and regional private satellite channels. Control of state media has provided a platform for SCAF’s narrative, which has emphasized rising chaos and its role in safeguarding the country from subterfuge and foreign interference. This has had the effect of tarring various political actors and activists who have sought to continue political mobilization and have tried to challenge SCAF. With broad swaths of the country fatigued by uncertainty and economic stress, tactical blunders, such as the disastrous decision to lead protests to the Ministry of Defense, have enabled SCAF to stigmatize its political opponents and burnish its popular reputation. So while state media is not in a position to explicitly endorse various candidates, such reactionary narratives push forward a political vision that benefits candidates associated with a return to law and order.

With the fraying of relations between SCAF and the Muslim Brotherhood, state media has recently turned its sights on Islamists, Egypt’s most powerful and organized political force. After having largely remained silent in the face of SCAF’s mismanagement and repression, the Brothers were hamstrung by a parliament with limited authority and a growing perception of political ineffectiveness and opportunism. The Muslim Brotherhood retains loyal support and has the advantage of a disciplined organization, but the shift in the tenor of coverage will likely have some impact on their prospects for electoral success.

Many observers also believe that SCAF has sought to manage competition by politicizing the state bureaucracy, namely through the work of the Supreme Presidential Elections Commission and the court system. Such allegations cannot be verified, but perceptions are important in terms of the legitimacy of the electoral process. The bureaucratic culling of the field of candidates has made the election a safer and less fraught process by disqualifying the most controversial and divisive candidates. However, the manner in which all three such candidates were disqualified raises questions regarding the propriety of the decisions. The disqualification of Hazem Salah Abu Ismail, the obscurantist Salafi demagogue with a dedicated popular following, was unremarkable as a legal matter. However, the decision was approached with caution because of its potentially destabilizing effects. The fact that the decision was complemented by the momentous disqualifications of Khairat El-Shater, the most powerful figure within the Muslim Brotherhood, and Omar Suleiman, the longtime head of intelligence and a close confidante of Mubarak, raised suspicions that the disqualifications had been grouped in such a manner as to immunize them from public scrutiny. Furthermore, the disqualification of El-Shater on the basis of a previous politicized conviction during the Mubarak era appears to be a questionable and overly narrow interpretation of the law to serve a political end. This series of disqualifications, including the surprising step to disallow Suleiman, seem to defy explanation on purely legal grounds.

Furthermore, the prospect that parliament will be dissolved by the Supreme Constitutional Court on the basis of a legal technicality is understood by political leaders as a clear threat from SCAF to the Egyptian political class. In recent discussions with political leaders, they indicated that in their private meetings with SCAF memberss the possible dissolution of parliament is a point of leverage in ongoing talks regarding the selection of a constituent assembly and the drafting of a new constitution. The independence of the judiciary is not even a point of theoretical consideration in these retellings. Within this environment it is impossible for elections not to be tainted by the manipulation and capture of the country’s institutional superstructure.

The backdrop for all these actions has been the continuing repression of political dissent that has marked SCAF’s tenure. While the boundaries of political expression have expanded tremendously since the fall of the old regime, SCAF has continued to employ military trials for civilians and has been accused of torturing detainees. Such repressive practices compromise the political climate and chill the ability to engage in protest and opposition activities.

SCAF is seeking to again act in extralegal fashion with respect to the country’s interim constitutional declaration. Perhaps the very first signal of SCAF’s undemocratic impulses was the unilateral issuance of a constitutional declaration, which departed in material and significant ways from the few amendments offered up in the March 2011 popular referendum, the country’s first democratic exercise. Due to the lack of a permanent constitution and the limitations of the interim document, an amendment to define the powers of the presidency is desirable, but SCAF seems intent on enacting such changes unilaterally and including controversial amendments to enshrine the autonomy and authority of the Egyptian military. This is yet another episode in which SCAF has diminished the democratic framework in which the presidential election is being held.

SCAF emerged from the fall of Mubarak with its power enhanced and its institutional rivals within the state diminished. But SCAF is not an effective strategic body, and its opaque, shifting, and repressive management of Egypt’s transition has alienated key political actors. Its often heavy-handed approach to asserting its own institutional prerogatives has made its heretofore untouchable privileges a topic of political discussion and contention. While the Egyptian military remains broadly popular with a majority of citizens and is still the most legitimate of Egyptian institutions, its tenure as the country’s interim authority has mobilized political opposition to the more far-reaching assertions of military power and authority. As has been displayed on the limited occasions of political cohesion, SCAF has been forced to amend its own designs when the Egyptian political class has taken unified stands.

However, as it prepares to transfer authority to popularly elected civilian leaders following a tumultuous period of transition, the Egyptian military is still the most potent political force in Egypt. The struggle to bound military power and to assert civilian supremacy will take years and is by no means assured. The presidential election is an historic milestone and a necessary prerequisite in that transition, establishing an additional center of elected authority. Following the hand over, SCAF will be forced to operate in more discreet fashion and its ambitions will be challenged by other political actors. But its approach to the presidential election should serve as an indication that SCAF will continue to exercise power selectively from behind the scenes and that limiting its political role and influence will be among the key tests for whether Egypt’s multi-year transition will be deemed a success.

Michael Wahid Hanna is a fellow at The Century Foundation. He focuses on issues of international security, human rights, post-conflict justice and U.S. foreign policy in the broader Middle East.