Tensions between Egypt’s majority Muslim community (or, at least, certain agitators within this community) and the country’s large Coptic Christian minority have simmered under the surface of Egyptian politics for decades. The sudden increase of sectarian violence since the January uprising, the most recent of which being the clash that left 26 dead on Sunday, has been interpreted by some as simply resulting from the absence of government suppression of unrest that was a hallmark of the Mubarak regime.

However, sectarianism and the stoking of sectarian tensions in Egypt is increasingly becoming a proxy for a broader struggle over the future of the post-Mubarak state. What may be most troubling is that the flaring of sectarian tensions is symptomatic of efforts to halt, or at least mitigate, the move to bring about thoroughgoing political reform in the country, with the army, venerated during the heady days of the Tahrir uprising, at the forefront of this effort.

A common theme of the reportage of the Egyptian uprising has been the esteem with which the Egyptian army is generally held across the country. Egypt is exceptional in the region in this regard, with the venerated status of the of the armed forces based on its role in the founding of the modern state during the early 19th century, through to its role in the overthrow of the British backed monarchy in 1952 Free Officers’ Coup and onward.

It was this coup that bought the military into direct confrontation with the Coptic community. Through the early 20th century, the Copts steadily expanded their control over the Egyptian private sector as well as within the nascent Egyptian parliament. After Nasser took control of the state in 1954, he instigated large-scale nationalisation programs, effectively undermining the Coptic domination of the Egyptian economy and replacing it in large part with military control over key industries.

Coptic resistance to this was exploited by some within the regime as representative of broader struggles between the radical nationalist agenda of the new Egyptian state and Western-backed elements seeking to reassert their control over Egypt’s vital industries. While this was not a uniform trend, with the vast majority of Egyptian Muslims and Christians coexisting peacefully, the sectarian issue became a political football that was kicked around when required for political expediency. When this happened, such as during Sadat’s Muslim revival period of the 1970s and the clashes between radical Islamists and Copts in Upper Egypt during the 1980s and 1990s, the resonant themes of Coptic exclusion from the state and suspicion over their allegiances framed the rhetoric.

In relation to Sunday’s events, and many instances of sectarian violence since January this year, it increasingly apparent that the army, or more specifically the Supreme Council of the Armed Forces (SCAF) who are caretaking the government until elections later this year, may be re-opening the sectarian issue as a pretext for clinging to power.

Sunday’s protests erupted in response to the burning of a Coptic Church in Upper Egypt and the absent official condemnation of this attack. While reports are still vague, it appears that as the protest gathered momentum through the streets of Cairo, agitators confronted the marchers by pelting them with stones and chanting anti-Coptic messages. When violence broke out between the two groups, the army drove personnel carriers directly into the protest group followed by direct fire on the crowd. The army’s official stance after the incident was that they were responding to protesters who had opened fire on the army, a line that has subsequently been taken back.

While this may seem like an unfortunate, but spontaneous event in what is still a highly fluid and volatile situation in Egypt, the official reporting of the incident gives reason for pause. State TV, current under the control of the SCAF, broadcast a direct message to viewers to take to the streets to defend the army from the “enemies of the state” as well as falsely reporting that the protesters had killed several army officers. Coptic leaders, and many within the Muslim community, have reacted angrily to this, claiming that this was a co-ordinated effort to re-open sectarian tensions and focus on the Coptic community as agents of foreign influence and to justify a continued military role in the governing of the state.

If so, this was a rather clumsy tactic on the part of the military, but one that sends a rather disturbing signal. Under Mubarak, the military controlled a significant proportion of the Egyptian economy, provided a chance of economic, political, and social mobility to even the poorest of Egypt’s citizens, and built a reputation as the so-called protectors of the people. However, as the negotiations over what post-Mubarak Egypt will look like, it appears that the remnants of the army’s old guard, the SCAF, are making a play for more overt control over the political process, perhaps fearful that any new arrangement will exclude them from future privileges.

In the process, they may be rending the bonds of community cohesion through exploiting sectarian tension, and destroying the military’s reputation as the only institution in the country that all Egyptians can trust. This is a dire development for a country in such a delicate position.