Egypt's first free parliament in six decades got to work on Monday with Islamists holding by far the most seats and opponents comparing their grip on the chamber to that enjoyed by the now defunct party of deposed President Hosni Mubarak.

With almost half the seats in the assembly, the Muslim Brotherhood is promising to cooperate with the military generals, who took power last February when Mubarak was overthrown, in their transition to civilian rule.

Thousands of protesters who fear a deal between the Islamists and the army to carve up power cried down with the military government behind a police cordon near the parliament building, a reminder to those trying to rebuild Egypt's state institutions of the power of the street.

A credible chamber would help Egypt's new political class prove it can govern and the Brotherhood has said it wants to be inclusive and ensure all voices in Egypt are heard.

The session began in sombre mood as parliament's acting speaker, automatically chosen as its oldest member, invited deputies to hold a silent prayer in memory of the hundreds who died in the uprising that ousted Mubarak in February last year.

The blood of the martyrs is what brought this day, said acting speaker Mahmoud al-Saqa, 81. Some deputies wore yellow sashes in protest at the army's policy to try thousands of civilians in military courts.

The session became more raucous when one Islamist member, Mamdouh Ismail, read the oath that vows allegiance to the nation and its laws but added his own words so long as it does not oppose God's law, prompting the acting speaker to tell him to repeat it without his addition.

An angry exchange erupted later as deputies worked on their first task of electing a speaker.

One candidate opposing Brotherhood nominee Mohamed Saad al-Katatni sought to introduce himself to the chamber, a move the Brotherhood opposed in a swift vote. Katatni, secretary-general of the Brotherhood's Freedom and Justice Party (FJP), was then appointed.

The two deputy speaker posts went to Ashraf Sabet Saad El-Deen of the Islamist al-Nour party, runners up in the vote, and Mohamed Abdel Aleem Dawoud of the liberal Wafd party.

We announce to the Egyptian people and the world that our revolution continues and we will not rest until all the revolution's goals are achieved, Katatni told the chamber, who thanked the army for fulfilling its promise to hold elections.

He pledged to serve all parliament without bias.

Opponents of the Brotherhood said its grip on parliament was similar to that enjoyed by Mubarak's National Democratic Party (NDP), which was handed large parliamentary majorities in widely discredited elections.

But unlike the NDP, the Brotherhood does not have an outright majority and must form alliances.

Hossam Hamalawy, a leftist activist, said: I do not have any high expectations for this parliament because of the composition of the political forces inside ... It seems they're going to reinvent the old regime with very few cosmetic changes.

PROTESTS

Many Egyptians, tired of a year of turmoil, want to give the army's promised transition a chance.

We won't see something worse than what we had ... I am one of the people ready to wait for change and I don't care if the military council is prosecuted or not, said Ahmed Hassan, a 28-year-old bank employee.

I want them to achieve the demands that led to the revolution, restore stability and security and get the economic wheel turning again, said accountant Elhamy Abdel Aleesm.

The generals will remain in charge until after a presidential election in June when they have promised to hand over power. Many Egyptians suspect the army may seek to retain influence behind the scenes.

The Brotherhood's rise marks a sea change from Mubarak's era when it was officially banned but won some seats by running candidates as independents.

It is unclear whether it will form a single bloc in parliament, which will have a role in drafting the new constitution by picking the 100-strong assembly that will draw up the document.

We will cooperate with everyone: with the political forces inside and outside parliament, with the interim government and with the military council until we reach safety heralded by a presidential election, said Essam el-Erian, deputy FJP head.

Liberals were pushed into third place behind the Freedom and Justice Party and the ultraconservative Islamist Salafis led by the al-Nour party. The FJP says it controls almost half the 498 elected seats, with a few re-runs to be held.

Monday's session marked the revival of an assembly that in the early 20th century was a vibrant forum for the nation's aspirations and filled with deputies who vied with the monarch and Egypt's British overlords.

Parliament's independent voice was extinguished after a 1952 coup that toppled the king and swept military-backed autocrats to power. Mubarak was a former air force commander and the ruling military council is now led by the man who was Mubarak's defence minister for 20 years, Mohamed Hussein Tantawi.

Mubarak's party routinely won sweeping majorities. The best performance by the Brotherhood was when it secured 20 percent of seats in the 2005 election. In 2010, almost all the opposition was all but squeezed out. The Brotherhood and other opponents boycotted what they saw as a blatantly rigged poll.

Mubarak, 83, is now on trial for his role in the deaths of 850 people during the uprising.

(Additional reporting by Tamim Elyan and Sherine El Madany; Writing by Edmund Blair and Tom Pfeiffer; Editing by Janet Lawrence)