Egypt’s military moved to curtail the powers of the country’s first freely elected president in more than half a century as early voting results suggest a win for the Muslim Brotherhood’s candidate Mohamed Morsi on Sunday.

Morsi was pitted against former prime minister Ahmed Shafik in a runoff election after the two came out on top in May’s first election round. The vote was necessary to replace former strongman Hosni Mubarak who resigned in February of last year after being in power for thirty years when tens of thousands took to the streets of Alexandria and Cairo to demand an end to military rule.

Mubarak sentenced last week to life long imprisonment for the crimes that were committed during the dying days of his regime.

The army has ruled the North African country on an interim basis since Mubarak resigned. Shafik, a former air force commander and aviation minister in Mubarak’s government, was seen as the military’s candidate. According to preliminary election results seen by the Muslim Brotherhood, Shafik won 48 percent of the vote compared to 52 for Morsi. Official results are expected to be released on Thursday.

It’s unclear exactly what role Egypt’s next president will have. The parliamentary panel that was appointed to rewrite Egypt’s constitution and refine the powers of the executive was disbanded last Thursday when Egypt’s highest court ruled a third of the parliamentary elections that took place between November and January unconstitutional, prompting the legislature to dissolve.

The Muslim Brotherhood, which had commanded a plurality of seats in parliament and a majority in coalition with other Islamists, denounced the court’s move as a “coup.” The military is now set to appoint a committee that will rewrite Egypt’s constitution.

The army’s attempts to curtail the growing influence of Islamists may be quietly welcomed by Egypt’s religious minorities and women who fear that the Brotherhood would seek to impose Islamist law but many of the revolutionaries who demonstrated in Cairo’s Tahrir Square are critical. They wanted a break with the past, something Shafik, in spite of his attempt to claim the mantle of the revolution and promises to defend civil liberties, evidently could not offer.

The army has pledged to hand power to the new president by July 1 but few expect the generals to give up the influence they hold over Egypt’s defense and foreign policy with it.