Women line up to vote at a polling station in Cairo, Egypt, on the second and final day of the run-off presidential election between Mohammed Morsi and former prime minister Ahmed Shafik on Sunday, June 17. 
Women line-up to cast their vote at a polling station in Cairo, Sunday. 
Egyptian Christian Coptic men help a woman reach a polling station in the Cairo Coptic Shubra neighborhood on Saturday, June 16. Voters returned to the polls after Egypt's Supreme Constitutional Court ruled Thursday that the Islamist-led Parliament must be immediately dissolved. 
An full veiled Egyptian woman casts her vote at a polling station in Cairo on June 16. 
Egyptians queue outside a polling station in Cairo. 
An Egyptian Muslim Salafist shows his ink-stained finger after voting a polling station. 
An Egyptian woman dips her finger in indelible ink after casting her ballot. 
Egyptian Muslim Brotherhood candidate Mohammed Morsi, center, waves to his supporters as he arrives at a polling station to vote in the city of Zagazig. 
An Egyptian woman casts her ballot in Cairo. 
Egyptians check to see their names are listed before casting their vote at a polling station 
Egyptian women dip their fingers in ink after voting at a polling station. 
An elderly Egyptian man shows the indelible ink stain on his finger after voting on the first day of the second round of the historical presidential election at a polling station in the city of Zagazig. 
Egyptians push a truck that was blocking the entrance of a polling station. 
An Egyptian man smiles after casting his vote in Giza. 
A veiled Egyptian woman looks for her name on the registered voters' list in the city of Zagazig. 
An Egyptian Coptic Christian woman casts her vote in the Cairo Coptic neighborhood of Shubra. 
Egyptian women cast their votes at a polling station. 
An Egyptian woman holds her baby as she prepares to vote at a polling station in Cairo. 
An Egyptian man shows off his little finger covered in indelible ink after casting his vote at a polling station in Cairo. 
An Egyptian man on his donkey shows his ink-stained finger after casting his ballot. 
Muslim Brotherhood candidate Mohammed Mursi casts his ballot at a polling station in the city of Zagazig. 
An Egyptian woman holds up an ink-stained finger after casting her vote at a polling station in Cairo. 
An elderly Egyptian man registers Saturday before voting in the city of Zagazig in an election that pits Ahmed Shafik, the last premier of ousted President Hosni Mubarak, against Muslim Brotherhood candidate Mohammed Morsi. 
Election officials and an Egyptian soldier direct voters during the second stage of runoff presidential elections at a polling station in Giza. 
Egyptian Christian Coptic men check the voters' list Saturday outside a polling station in the Cairo Coptic neighborhood of Shubra. 
Egyptians burn the likeness of presidential candidate and former Prime Minister Ahmed Shafik in Cairo on Friday, the eve of the nation's presidential election. 
A bus driver stops to wave in support of Egyptian protesters making their way to Tahrir Square on Thursday. 
Egyptians pray in Tahrir Square on Thursday during a protest against presidential candidate Ahmed Shafik. 
A protester stands on a barricade of barbed wire as Egyptian military police stand guard. Egypt's Supreme Constitutional Court ruled that the Islamist-led parliament must be immediately dissolved. 
An Egyptian boy waves his shoes as he joins supporters of the Muslim Brotherhood in a protest in Cairo's Tahrir Square against Mubarak-era prime minister and presidential candidate Ahmed Shafik after Egypt's top court rejected on Thursday a law barring him from standing in a tense presidential poll runoff. 
Protestors gesture towards military police through a barricade of barbed wire during a protest against presidential candidate Ahmed Shafik outside the Supreme Constitutional Court on Thursday. 
People walk past graffiti showing faces of ousted Egyptian president Hosni Mubarak, right; Field Marshal Hussein Tantawi, second right; former Secretary General of the Arab League Amr Mussa, second left, and former prime minister and presidential candidate Ahmed Shafiq, left, at Tahrir square. 
A boy peers through barbed wire at Egyptian military police standing guard outside the Constitutional Court in Cairo on Thursday, June 14. 
Egyptian women line up to cast their vote Saturday. 
Presidential candidate Mohamed Morsi of the Muslim Brotherhood, who is set for a runoff election against Ahmed Shafiq, speaks at a press conference in Cairo on Wednesday, June 13. 
Former Prime Minister Ahmed Shafiq, center, is seated before addressing a business conference in Cairo on Wednesday. 
Egyptians read the front page of newspapers for sale outside of Al-Fatah Mosque in Cairo on Friday, May 25. 
Ballots are counted by election officials in Alexandria as the country eagerly awaits the outcome Friday. 
A supporter of presidential candidate Abdelmonen Abol Fotoh voices her opinions at Tahrir Square on Friday. 
Supporters of various candidates debate outside Al-Fatah Mosque in Cairo on Friday. 
Electoral officials monitor voting in Namul, a village north of Cairo, on Thursday, May 24, the second and final day of voting in Egypt's historic presidential election. Egypt is holding its first presidential election since last year's toppling of Hosni Mubarak, part of the wave of Arab Spring uprisings. 
Egyptian women wait in line Thursday to cast their vote outside a polling station in Cairo. If no candidate gets a majority of the vote in the first round of voting, a second round will be held June 16-17. 
An election worker checks the identification of a voter at a polling place Thursday in Namul as Egyptian soldiers stand guard. 
A soldier stands watch in the Egyptian capital on the second day of voting. A pervasive fear exists that the powerful military, which has run the country since Mubarak's fall 16 months ago, could try to hijack the election. 
An Egyptian man waits to cast his ballot Thursday north of Cairo. The vote is considered Egypt's first free and fair presidential election in modern history. 
An Egyptian man drops off his ballot at a polling station Thursday in Cairo. The voting marks the first time Egypt has held a presidential election in which the results aren't known beforehand. 
An Egyptian woman holds up an ink-stained finger after casting her ballot in Cairo on Wednesday, May 23, the first day of voting in the historic election. 
A voter studies her ballot Wednesday in Cairo. Thirteen candidates are competing in the wide-open race, but two withdrew after ballots were printed. 
Egyptian men fill out their ballots Wednesday in Cairo. Results of the first round of voting are not expected before the weekend. 
An Egyptian man casts his ballot at a Cairo polling station. Some Egyptians told CNN that they waited up to four hours Wednesday to vote. 
Egyptian men shield themselves from the hot sun outside a Cairo polling station Wednesday. 
Egyptian men line up to cast their vote Wednesday in Cairo. Some 30,000 volunteers fanned out to ensure voting is fair, said organizers with the April 6 youth movement, which has campaigned for greater democracy in Egypt. 
Egyptian men fill out their ballots at a Cairo polling place. 
Presidential candidate Hamdeen Sabahy, a leftist dark-horse contender, flashes a sign of victory as he waits to vote at a Cairo school. 
Presidential candidate Abdelmonen Abol Fotoh, a moderate Islamist, casts his ballot Wednesday in Cairo. 
An Egyptian Coptic nun drops her ballot at a Cairo polling station Wednesday. 
Egyptian women wait outside a polling station in Cairo. Many Egyptians seem uncertain of their loyalties to any particular candidate. 
- NEW: The Muslim Brotherhood says its candidate won with 52.5% of the overall vote
- NEW: A count by state media shows Morsi ahead, but with millions still to be counted
- Shafik's campaign accuses the Muslim Brotherhood of systemic election fraud
- Military leaders say they will retain legislative power until a new parliament is picked
Cairo (CNN) -- The Muslim Brotherhood declared that its candidate won Egypt's historic presidential election this weekend, making the claim hours after openly challenging the nation's military rulers over its dissolution of parliament.
With several million votes still to be counted, the state-run Al-Ahram news website around 4:15 a.m. Monday (10:15 p.m. Sunday ET ) showed the Brotherhood's Mohamed Morsi leading with about 5,648,000 votes compared with about 4,705,000 for opponent Ahmed Shafik, who served as Egypt's last prime minister in the waning days of Hosni Mubarak's regime.
Yet the Islamist group, citing what it said were all-but-complete official numbers released to its representatives at polling stations nationwide, asserted that Morsi had won by capturing 52.5% of the overall vote.
The official vote count was scheduled to be finished at some point Monday, with finals results to be announced Thursday.
Whoever they declare the winner will become the North African nation's first president since Mubarak, who was ousted in a wave of popular unrest last year after three decades in power.
The next president will wade into a country with a political system mired in controversy, confusion and confrontation, much of it due to events over the past week.
Egypt has no constitution in place, though military rulers have vowed to appoint a 100-person panel to craft such a document. And a court ruling just days before the runoff appeared to invalidate an Islamist-dominated legislative body and then saw the military swiftly move to dissolve that parliament ahead of the election.
Egypt's political storm intensifies 
Egyptian street fighter vies for change 
Debate booming among Egypt's voters 
Egyptian: 'Revolution has long way to go' But the Muslim Brotherhood, whose Freedom and Justice Party had won a majority of legislative seats, is bucking this act to dissolve parliament.
Mahmoud Ghozlan, a spokesman for the Islamist group, called the move "unconstitutional" and said parliamentary speaker Mohamed al-Katatni will convene legislators on Tuesday.
"This parliament was chosen by 30 million voters over a period of three months, and the legislative power was handed to (lawmakers) chosen by the people," Ghozlan said. "It is unconstitutional to dissolve it."
And Hussein Ibrahim, a Brotherhood member and majority leader in the legislature, insisted Sunday that parliament "has not been dissolved," according to a report from the state-run Al-Ahram news agency.
Vowing the Brotherhood won't "give it to a coup d'etat," Ibrahim said while casting his vote in Alexandria that military rulers must respect a March 30 constitutional declaration that gives only "the people" the authority to dissolve parliament.
The Supreme Council of the Armed Forces, meanwhile, issued a new constitutional declaration Sunday night detailing some powers that the new president will hold, but gave little indication it was budging on the state of parliament.
After being sworn in, the new president will set the date for parliamentary elections and can pardon and appoint government officials and ambassadors to foreign countries.
But the military leadership stated that legislative power, as well as control of the national budget, will remain in its hands until a new parliament is elected.
The Brotherhood "strongly rejected" the military declaration about parliament on its official Twitter feed. The group also said that the constitutional panel picked by parliament will hold its first meeting Monday to begin drafting a constitution, in defiance of the military council.
There's also plenty of dispute over the validity of this weekend's presidential runoff vote, which Shafik and Morsi's campaigns accusing each other of election fraud.
A wild election weekend for Egypt, France and Greece
Turnout appeared sluggish Sunday at some polling stations in Cairo, where streets were mostly quiet despite what many Egyptians viewed as moves last week by military leaders, who have ruled the country since Mubarak was forced out in February 2011, to hold on to power. Some voters may have stayed home because of sweltering heat, officials told the state-run Al-Ahram newspaper.
As of 4 p.m. Sunday in Egypt, 40% of the nation's 50 million eligible voters had cast ballots, according to Farouk Sultan, the head of Egypt's Supreme Presidential Election Commission. In the first round of voting last month, 46% of voters participated.
Officials have reported few voting irregularities in the second round of elections, Sultan said.
To protect the balloting process, authorities went so far as to camp outside polling stations overnight during the runoff. At one station designated for women in Cairo, guards slept on the doorstep.
The Supreme Presidential Electoral Committee approved licenses for 53 organizations to observe the elections, including at least three international groups -- the U.S.-based Carter Center, the South Africa-based Electoral Institute for Sustainable Democracy in Africa and the Arab Network for Monitoring of Elections.
Yet Shafik's campaign filed "several complaints" with Sultan's commission, alleging the Muslim Brotherhood committed "systemic violations."
Specifically, they accused the Islamist group's supporters of bribing voters with "large sums of money and food" to back Morsi, as well as using "intimidation, threats and violence against supporters of candidate Ahmed Shafik." The former prime minister's camp also said it "filed more than 100 official complaints accusing the Brotherhood of ballot rigging and stuffing."
"The Muslim Brotherhood's systematic election violations prove how the (group) does not believe in freedom of choice and democracy unless this democracy brings them to power," Shafik's campaign said in a statement. "The organized and persistent election fraud by the Muslim Brotherhood proves they ... only talk the talk and never walk the walk of liberal democracy."
In a statement on its website, the Brotherhood flatly denied what it called "false reports being circulated" and urged election officials to promptly investigate what it called "games and plots." It also accused "the rival candidate's supporters (of) paying cash bribes to some voters," among other allegations.
Outside the city, in Giza, Mohammed Gamea cast his ballot for Morsi even as he questioned whether the election was fairly handled.
"I don't believe the Egyptian presidential elections are fair to begin with," he said Sunday morning. "The military council, assisted by the elections committee, tried everything to stall and influence the process, from disqualifying previous candidates before the first round -- not to mention the negative campaigns against Morsi -- while keeping quiet about Shafik."
"But despite all (this), I don't believe that there has been any electoral fraud. The ballots will determine what is next for Egypt."
The real obstacle to democracy in Egypt
Some disgruntled voters launched a campaign to invalidate ballots, said Mohamed Ghoneim, the founder of a group that marked "X" on the names of both Morsi and Shafik, thereby nullifying their vote.
Among the boycotters was Mohamed Khamees, who said he lost sight in his left eye from a police beating in Tahrir Square during the early 2011 protests.
"If I give this country for the Brotherhood hands, there is not going to be any more Egypt, it will be destroyed," he told CNN. "And if I give it to someone from the old system, it looks like we did nothing."
What is the Muslim Brotherhood?
CNN's Saad Abedine, Ivan Watson and Ben Wedeman and journalists Mohamed Fadel Fahmy and Ian Lee contributed to this report.
