* Polls open in two-day election, Sisi set to win
* Vote marks 7th election or referendum since Mubarak toppled
* Sisi seen as hero to supporters, villain to opponents
* Protests flare near Cairo, in Alexandria (Adds protests)
By Stephen Kalin and Shadia Nasralla
CAIRO/SUEZ, May 26 (Reuters) - Egyptians voted on Monday in an election expected to install army chief Abdel Fatah al-Sisi as president, with supporters brushing aside concerns about political freedom and hailing him as the strong leader the country needs.
Three years after the historic uprising against Hosni Mubarak, the vote is set to restore a pattern of rule by men from the military after Sisi toppled Egypt's first freely elected leader, Mohamed Mursi of the Muslim Brotherhood.
Voters lined up to cast ballots at polling stations guarded by soldiers in face masks and armed with assault rifles. Sisi faces only one challenger in the two-day vote: the leftist politician Hamdeen Sabahi.
"We see Sisi as a real man. Egypt likes a strong man," said 64-year-old Saber Habib, clenching his fist to make his point as he waited to vote in the city of Suez, east of Cairo.
"We want the country to move forward and for the people to have bread," said Habib, a contractor.
Widely regarded as Egypt's de facto leader since he toppled Mursi after mass protests, Sisi, 59, faces manifold challenges including an economy in crisis and a campaign of Islamist violence that has spiralled since he overthrew Mursi.
To the Islamists, he is the mastermind of a bloody coup that led to a crackdown that has killed hundreds of Mursi supporters and landed thousands more in jail. Secular dissidents who led the 2011 uprising against Mubarak have also been imprisoned.
At the same time, several hundred members of the security forces have been killed in a campaign of violence by radical Islamists since last July. The last year has been the bloodiest period of internal strife in Egypt's modern history.
The Brotherhood and its allies have called for a boycott, declaring it "the election of the presidency of blood". Eleven of the group's supporters were arrested while staging a protest in Alexandria, Egypt's second city, security officials said.
The government says the Brotherhood is a terrorist organisation.
As he voted in Cairo, Sisi waved to supporters, who shouted "President, President!"
"Today Egyptians are going to write their history," said Sisi, who hopes a big turnout will give him a strong mandate.
The election is the seventh vote or referendum since the 2011 uprising that raised hopes for democracy. But three years on, with democracy seen as an experiment that failed, many Egyptians say stability comes first.
Sisi won 95 percent of votes cast in advance by Egyptians overseas, but an opinion poll by the Washington-based Pew Research Center suggests a more mixed picture, with Sisi viewed favourably by 54 percent and unfavourably by 45 percent.
At one polling station reserved for male voters in Cairo, all bar one person in a line of around 50 said they would vote for Sisi, who has been lionized by media run by the state and big businessmen overwhelmingly supportive of the army.
"I'm voting for Sabahi because of his programme and because Egypt needs a civilian president to begin building a democratic society like other countries have," said Fathi Abdelhamid, 58, a manager at an engineering firm.
Interrupting him, the person next to him said: "But most people want someone with experience, and that person is Sisi. Look at his experience in military intelligence. He knows how to work with the state."
Since the army overthrew the king in 1952, Egypt has been ruled by a succession of military men - Gamal Abdel Nasser, Anwar Sadat and Mubarak. That pattern was briefly interrupted by Mursi's divisive year in office, during which important institutions of state resisted his authority.
The 2012 election won by Mursi was contested by around a dozen candidates, in stark contrast to this vote.
"What happened in Egypt was wrong and the best message against it is to boycott this vote," said Abdel Karim Mohamed, a 45-year old accountant, speaking in hushed tones as he parked his motor-bike near a polling station.
Witnesses and security officials said 400 Mursi supporters staged a march against the election in Kerdasa, a town on the Cairo outskirts where 14 policemen were killed in an attack last August after the security forces killed hundreds of Mursi supporters.
An influential Muslim cleric with Brotherhood links urged Egyptians to boycott the vote. Sheikh Youssef al-Qaradawi, who lives in Qatar, said Sisi had "disobeyed God".
Critics fear Sisi will rule Egypt with an iron fist.
Human rights groups have raised serious concerns about accounts of torture in police custody, and a court's decision to sentence some 1,200 Brotherhood supporters and members to death earlier this year drew criticism from Western governments.
In an interview with Reuters, a former Muslim Brotherhood leader warned that government oppression was fanning militancy that will pose a threat abroad unless the army-backed authorities start respecting freedom and human rights.
"There is no option for any government in Egypt other than to bring about national reconciliation," said Abdel Moneim Abol Fotouh. "The injustices must stop."
"Egypt's presidential elections will not wipe the country's human rights record clean after 10 months of gross violations," rights group Amnesty International said in a statement.
Sisi has listed security and the economy as his primary concerns and said Egypt is not ready for a Western-style democracy - a view with echoes of the Mubarak days.
The election will have a bearing on relations with the United States, which has linked the future of its long-standing military ties with Cairo to the political transition.
Following Mursi's overthrow and the crackdown, the Obama administration suspended much of its $1.3 billion in annual military aid to Cairo. But last month it announced it would resume some of the aid, partly to help in the fight against militants.
Monitors from the European Union and U.S.-funded Democracy International are observing the vote, and more than 400,000 members of the security forces have been deployed to secure polling stations across the country.
As voting began, one of Egypt's state-run TV stations reported a bomb had exploded outside a polling station. The Interior Ministry denied the report, saying the noise was a car back-firing. (Additional reporting by Maggie Fick, Yasmine Saleh and Asma Alsharif; Writing by Tom Perry; Editing by Giles Elgood)