CAIRO -- Muslim Brotherhood candidate Mohammed Morsi claimed a narrow victory early Monday in Egypt’s first free presidential election, hours after the ruling military council further expanded its control over the country by granting itself war powers, raising new questions about what authority the president would actually have.

Morsi’s declaration of victory at 4 a.m. local time, six hours after polls closed, set the stage for a protracted conflict between the Brotherhood, Egypt’s best organized political party, and the military establishment and allies of deposed President Hosni Mubarak, who have ruled the modern Egyptian state since its inception.

Morsi’s election rival, Ahmed Shafik, who served as Mubarak’s last prime minister, said he didn’t accept the result. Morsi claimed that he had won 52 percent of the vote with 97 percent of precincts reporting, based on reports from party representatives who were observing vote counting at polling stations across Egypt. Egypt’s official election commission had yet to issue its own count, but the Brotherhood’s preliminary tallies proved largely accurate in last month’s first-round presidential vote.

By swiftly declaring victory, the Brotherhood appeared to be pushing back against the military’s efforts in recent weeks to consolidate its hold over Egypt. What was once celebrated as a revolution that toppled Mubarak and could have inspired the Arab world has increasingly become a counter-revolution by the ruling generals, who have reinstated martial law, dissolved the Muslim Brotherhood-dominated Parliament and will control who writes Egypt’s new constitution.

For the second time in less than a week, the military council issued a decree that greatly enhanced its already near-total power: it amended the temporary constitution to define the powers of the president and gave itself the final say over major military matters. Under the change, president can’t declare war without the military council’s approval, and the council itself will decide its commanders. In the absence of a Parliament, the new president will take the oath of office before the Supreme Constitutional Court, which consists of Mubarak appointees.

Even before the military council’s announcement, the two-day runoff vote that ended at 10 p.m. Sunday was shrouded in suspicion over the generals’ intentions, with many Egyptians convinced that it would ensure a victory for Shafik. The Brotherhood, which held 47 percent of seats in the now-dissolved Parliament, has increasingly clashed with the generals and on Sunday seemed to signal that it would protest if Shafik was declared the winner.

The sense of uncertainty dampened voter turnout. The Brotherhood’s tally said that about 24 million votes were cast out of a population of 50 million eligible voters.

The election commission council said that final results would be announced later this week, but the series of moves by the military made it clear that voters had elected a president without knowing what his powers would be.

In the days leading up to the runoff, the military council named itself in charge of the legislative branch after the constitutional court ruled that some parliament members had been elected illegally. With that, the constitutional assembly, which was to consist of Egyptians and parliamentarians tasked to write the new document, was now under control of the generals. The generals announced Sunday that an assembly will write the permanent constitution within three months of being named, and the document will be put before a public referendum within 15 days. The composition of the constitutional assembly remained unclear.