Islamists aimed to cement control over Egypt's lower house of parliament as a final phase of voting began on Tuesday, while a secular party's plan to boycott elections for the upper chamber threatened to weaken the liberal bloc.

Banned under Hosni Mubarak, the Muslim Brotherhood has emerged as a major winner from the uprising that toppled him, exploiting a well-organised support base in the first free legislative vote in decades.

Islamists of various stripes are expected to win 60 percent of the 498-seat lower house, with the Brotherhood taking some 41 percent, by its own count.

Run-offs scheduled to take place on Tuesday and Wednesday and reruns in parts of Cairo, Alexandria and other cities where the vote was cancelled in the first round due to irregularities, are set to fill the 11 percent of seats as yet undecided, according to Brotherhood figures.

The outcome of the runoffs and reruns are unlikely, however, to alter the dominance of the Islamists who now look set to wield major influence over the shape of a new constitution to be drafted by 100-strong body that the new assembly will pick.

The Brotherhood has promised that Egyptians of all persuasions will have their say. The strong Islamist performance has alarmed some liberal Egyptians and Western governments that backed Mubarak, but it is far from clear whether rival Islamists will form any alliance in the new assembly.

With the exception of the parties that are part of our coalition, we stand at an equal distance from all parties, Essam al-Erian, deputy head of the Muslim Brotherhood's Freedom and Justice Party, told Reuters.

So far, we have begun limited consultations to gather the opinions of the blocs, parliamentary bodies and different parties but I will not announce these alliances until before parliament sits.

Egypt's staggered three-stage parliamentary election began on November 28 and drew an unprecedented turnout. Under a complex system, a third of the seats are reserved for individuals, and some of these will be decided in the runoffs. The other two thirds are decided by proportional representation among party lists. The lower house will hold its first session on January 23.

Elections to the advisory upper chamber, or Shura Council, begin at the end of January and continue into February. The military generals, who assumed Mubarak's powers after he was swept from office last February, will rule until the end of June, by which time they say the country will have elected a new president to whom they will hand power.

PARTY BOYCOTT

Despite the Brotherhood's assurances, the strong Islamist showing has caused consternation among liberal opponents and Tuesday's run-offs were overshadowed by one party's surprise decision to boycott elections for the Shura Council.

The Free Egyptians Party (FEP) co-founded by telecom tycoon Naguib Sawiris said it would boycott in protest against what it said were violations committed by Islamist parties in earlier voting rounds.

The withdrawal of the FEP could be a major blow to the Egyptian Bloc, an alliance of liberal and leftist groups of which it is a key member and which is expected to win some nine percent of seats in the lower house, putting it in third or fourth place.

The bloc has attracted Christian and secular voters, but non-religious parties have emerged as the weakest players in the new political game.

The process has turned into a religious competition rather than an electoral one, which amounts to a forging of awareness whose effect on the results is no less than the physical forging that used to happen, the FEP said in a statement.

Local monitors have said Egypt's first free parliamentary vote since army officers overthrew the monarchy in 1952 has been marred by minor violations that could cast doubt on the results of some constituencies, but that the infractions would not undermine the legitimacy of the ballot as a whole.

The FEP called on other parties to join it in boycotting the Shura Council election and it was not immediately clear whether the Egyptian Bloc would run without one of its main parties.

A broader liberal boycott would leave Egyptian politics firmly in the hands of the Islamists and the military, with whom the Brotherhood has pledged to cooperate during a transition that youth groups would like to see speeded up.

(Additional reporting by Tamim Elyan and Tom Perry; editing by Rosalind Russell)