An election committee source told Reuters that Islamist Mohamed Mursi, a United States-trained engineer, was comfortably ahead of former air force General Ahmed Shafik with most of the votes tallied, but that the count had yet to be officially finalised.
However, new head of state is likely to remain subordinate to the military for some time at least. In yet another twist in Egypt's tortuous path from revolution to democracy, the ruling military council issued a decree as voting ended on Sunday that set strict limits on the president's powers. On the eve of the election, it had already dissolved the Islamist-led parliament.
Liberal and Islamist opponents denounced a "military coup".
The chaotic end to the race, as Shafik's camp challenged the Brotherhood's claim overnight, and the last-minute intervention by the generals who pushed out Mubarak in the name of the people, were in keeping with a transition that was meant to chart a new course for the Arab world's most populous nation but has left most of the 82 million Egyptians weary and confused.
Both Egypt's Western allies, long wary of the rise of political Islam, as well as neighbouring Israel, worried about its 1979 peace treaty with Cairo, have looked on with alarm as its economy totters and hostile rhetoric gets a wider airing.
"Mohamed Mursi is the first popularly elected civilian president of Egypt," the official website of Brotherhood's Freedom and Justice Party announced in the early hours of Monday.
But an aide to Shafik, an ex-military man like Mubarak, contested that and said the group was "hijacking the election."
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