Updated at 11:09 p.m. ET: As Egyptians waited for the results of the presidential election, the ruling military council issued new rules that made clear the real power remains with the army.

The Muslim Brotherhood's party on Monday declared its candidate, Mohammed Morsi, had won the country's first free presidential election, defeating Ahmed Shafik, ousted president Hosni Mubarak's last prime minister.

But at Shafik's campaign headquarters, Ahmed Sarhan said: "I do not accept this, I will not file wrong numbers." However, another campaigner said: "I don't think we will make it." One woman campaigner at Shafik's headquarters was in tears.

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Egyptian supporters celebrate the apparent victory of their presidential candidate Mohamed Morsi, in Tahrir Square, Cairo on Monday.

Hours earlier, the Supreme Council of the Armed Forces (SCAF) issued a decree granting itself broad power over the future government, diminishing the authority of the president and seizing control of the process of writing a permanent constitution, The New York Times reported.

The move is the latest in a series of steps that the military has taken recently to hold on to power they had promised to hand over to elected civilians, the Times reported.

The military council's "constitutional declaration" -- issued under powers it took for itself after pushing aside Mubarak to appease street protests 16 months ago -- was a blow to democracy, said many who aired their grievances on social media, a favored weapon in the Arab Spring that ended Mubarak's 30-year rule.

'Outright military coup'
"Grave setback for democracy and revolution," tweeted former U.N. diplomat and Nobel peace laureate Mohamed ElBaradei.

"SCAF retains legislative power, strips president of any authority over army and solidifies its control," he added.

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Egyptian election workers count votes at a polling station on June 17, in Cairo.

"The 'unconstitutional declaration' continues an outright military coup," tweeted Abdel Moneim Abol Fotouh, a moderate Islamist knocked out in the first round of the presidential election last month. "We have a duty to confront it."

A Facebook page whose young activists helped launch the uprising mocked the army's order, noting Egypt would have a head of state with no control over his own armed forces: "It means the president is elected but has no power," one comment read.

Turnout, which was only 46 percent in the first round of the presidential vote, appeared to electoral officials to have been no higher for the decisive head-to-head contest.

Many of the 50 million eligible voters were dismayed by an unpalatable choice between a man seen as an heir to Mubarak and the nominee of a religious party committed to reversing liberal social traditions. Some cast a ballot against both men in protest.

In a victory speech at his campaign headquarters, Morsi clearly sought to assuage the fears of the large sector of Egyptians that the Brotherhood will try to impose stricter provisions of Islamic law.

"Thank God, who guided the people of Egypt to this right path, the path of freedom and democracy," the bearded, 60-year-old U.S.-educated engineer declared, promising to "be a president for all Egyptians".

He mentioned churches and Christians several times and hardly mentioned Islam or Muslims.

The order from Field Marshal Hussein Tantawi, the chairman to the Supreme Council, indicated that the army, which also controls swathes of Egypt's economy, has no intention of handing substantial power now to its old adversary, the Brotherhood.

"SCAF will carry legislative responsibilities ... until a new parliament is elected," the council's order said.

It raised a question of how, even if a civilian head of state is sworn in this week, Tantawi can claim to have met his own deadline of July 1 for relinquishing control -- a deadline the armed forces' major patron and paymaster the United States had stressed in recent days it was expecting him to respect.

Washington and Egypt's European allies, also major providers of aid to the most populous Arab state, had voiced concern when Tantawi, backed by a judicial ruling from a court appointed under Mubarak, dissolved the parliament elected in January in which the Brotherhood and hardline Islamists had a big majority.

'Dangerous days'
The Brotherhood has rejected the army's power to dissolve parliament and warned of "dangerous days."

But though some have compared events to those in Algeria 20 years ago, which ended in civil war between the military and Islamists, many doubt that the Brotherhood has an appetite for violence at present.

Many opponents of military rule have also complained that the Brotherhood has overreached itself in seeking both legislative and presidential power.

Egyptians massed in their millions against Mubarak in January last year in the hope that his removal would end poverty, corruption and police brutality. Many now seem tired of the social turmoil and political bickering that ensued.

Egypt's armed forces have built up massive wealth and commercial interests, helped since the 1970s by a close U.S. alliance which followed the decision of the most populous Arab state to make peace with Israel.

Many Egyptians say the army is just one wing of an entrenched security establishment that has resisted reform and oversight since Mubarak left and would wield influence long after the promised handover to an elected civilian.

"There is no doubt that the state in all its institutions -- judicial, military, interior, foreign and financial -- back Shafiq for president and are working to that end," said Hassan Nafaa, a politics professor who campaigned against Mubarak.

"It is very difficult to eradicate this spirit of Mubarak."

Reuters and the Associated Pres contributed to this report.

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Egyptian security forces help a woman after she voted at a polling station in Cairo on Sunday.

Updated at 9:16 p.m. ET: CAIRO - Egyptians anxiously waited for their first freely elected president on Sunday after two days of voting that was to be the culmination of their Arab Spring revolution but which many fear may now only compound political and economic uncertainty.

The Muslim Brotherhood said on Monday that its candidate, Mohammed Morsi, was holding on to a lead of 54 percent with 90 percent of the polling stations counted, Reuters reported. Morsi's rival, ex-military man Ahmed Shafiq had 46 percent of the votes counted, the Brotherhood official told Reuters.

Each campaign is allowed to have representatives in polling stations to watch the count.

In a country unused to free elections, it was unclear when the official final result would emerge. After a first round of voting last month, which knocked out several popular candidates, it took several hours.

On Monday, the new president, whether Morsi or Shafiq, will be told, along with the rest of the country, what powers he will have by the ruling generals. Military and legal sources told Reuters the military council would take back legislative powers for now from a new, Islamist-dominated parliament that it has dissolved following a court ruling voiding an earlier election.

Turnout, which was only 46 percent in the first round of the presidential vote, appeared to electoral officials to have been no higher for the decisive head-to-head contest. Many of the 50 million eligible voters were dismayed by an unpalatable choice between a man seen as an heir to Mubarak and the nominee of a religious party committed to reversing liberal social traditions. Some cast a ballot against both men in protest.

"I'll cross out both Morsi and Shafiq because neither deserves to be president," said Saleh Ashour, 40, a shopkeeper in the middle-class Cairo neighborhood of Dokki as he went to vote. "I want to make a statement by crossing out the two names.

"Just staying away is too passive."

Shafiq, 70, had promised he had heeded the lessons of the revolution 16 months ago and offered security and prosperity. Morsi, 60, tried to widen his appeal beyond the Brotherhood's committed and disciplined base by pledging to preserve a pluralist democracy and finally end a history of military rule.

In the second city, Alexandria, computer engineer Sameh Youssef, 30, was wary of Islamist rule but wanted to honor the dead of an uprising launched by frustrated young urbanites: "I will vote Morsi," he said. "Not because I like him but because I hate Shafiq. Between us and Shafiq there is blood."

In Old Cairo, however, 56-year-old physician Khalil Nagih echoed the sentiments of many, including Christians like himself, whose mistrust of the Brotherhood and desire for an end to a year of chaos outweighed anxiety about the army's role:

"I chose Shafiq because he has experience of administration and was an officer. He is a straight talker and he speaks to all communities. He says he'll solve our problems and I believe him. Morsi will bring a religious state and take Egypt backwards."

In Egypt vote, little enthusiasm for presidential finalists

Whoever wins, Egypt's political landscape is hazy beyond one clear landmark - the 20 or so senior commanders around Field Marshal Hussein Tantawi, whose Supreme Council of the Armed Forces (SCAF) claimed sovereign power after easing out their brother officer Mubarak to appease the millions on the streets.

In what opponents denounced as "coup", the SCAF dissolved parliament after judges, appointed under Mubarak, ruled on Thursday that a legislative election over the winter breached legal rules and would have to be re-run.

The Brotherhood and hardline Islamist allies dominated the new chamber, and risk losing seats in any new vote, having alienated many outside their core support base. Among failings they are accused of was the inability to form a consensus body to draw up the new constitution Egyptians are hoping for.

As presidential voting was ending, military and legal sources told Reuters that the military council would promulgate an amended constitutional decree on Monday returning to itself the legislative powers it handed to parliament this year.

"In the absence of parliament, legislative powers move back to the military council, which has been in charge of the country and will hand over presidential powers to the president soon," a military source told Reuters.

The decree would also define the new president's powers: "The country's head of state will have the power to appoint a prime minister and cabinet ministers," the military source said.

A lawyer who attended a meeting with the military council on Sunday said: "The presidential powers which the military council held until now will now shift to the new president."

The Brotherhood has rejected the army's power to dissolve parliament and warned of "dangerous days". But though some have compared events to those in Algeria 20 years which ended in civil war between the military and Islamists, many doubt that the Brotherhood has an appetite for violence at present.

Egyptians protest against old regime day before presidential election

Many opponents of military rule have also complained that the Brotherhood has overreached itself in seeking both legislative and presidential power, limiting its broader appeal.

Egyptians massed in their millions against Mubarak in January last year in the hope that his removal would end poverty, corruption and police brutality. Many now seem tired of the social turmoil and political bickering that ensued.

"Egypt writes the closing chapter of the Arab Spring," read a headline on Sunday in independent newspaper al-Watan, which said the election offers a "choice between a military man who aborted the revolution and a Muslim Brother who wasted it."

Monitors said they had seen only minor and scattered breaches of election rules by Sunday morning but not the kind of systematic fraud that tainted elections under Mubarak, despite mutual accusations of irregularities by the rival camps.

A win for Shafiq may prompt street protests by the Islamists and some of the disillusioned urban youths who made Cairo's Tahrir Square their battleground last year. Should Morsi prevail, he may be frustrated by an uncooperative military elite, for all the generals' pledges to cede power by July 1.

Egypt's armed forces have built up massive wealth and commercial interests, helped since the 1970s by a close U.S. alliance which followed the decision of the most populous Arab state to make peace with Israel.

Many Egyptians say the army is just one wing of an entrenched security establishment that has resisted reform and oversight since Mubarak left and would wield influence long after the promised handover to an elected civilian.

"There is no doubt that the state in all its institutions - judicial, military, interior, foreign and financial - back Shafiq for president and are working to that end," said Hassan Nafaa, a politics professor who campaigned against Mubarak.

"It is very difficult to eradicate this spirit of Mubarak."

Reuters and The Associated Press contributed to this report.

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Follow us on Twitter: @msnbc_world