Witnesses told the Evening Standard that the Islamist party, which is expected to secure a large share of the votes, had a strong presence both inside and outside polling stations.
Onlookers claimed some Brotherhood groups were allowed to set up tables with laptop computers in order to show “people how to vote”.
Voting laws passed after the fall of Hosni Mubarak’s regime in February outlaw bribes or campaigning inside or near polling stations.
Today voting continued with turnout again reported to be high. Student Mariam, who would not give her full name for fear of reprisals said: “I wanted to boycott the elections, as the parliament will have no power and because of what happened in Tahrir, but if we don’t vote the Muslim Brotherhood will win the majority.”
But there is growing support for the Muslim Brotherhood with many claiming the party is the best option to bring order to Egypt.
“The Freedom and Justice Party (Muslim Brotherhood) are the most organised party right now,” said Hossam, 39, an insurance broker who went to a Catholic school in Cairo.
“They have a religious view but they are the only ones who have a good plan for the country.” The outcome of the election will indicate whether Egypt will remain secular or move down an Islamic path as have other countries swept up in the Arab Spring.
Zeinab Saad, 50, said: “I am voting for this country’s sake. We want a new beginning. Its a great thing to feel like your vote matters.”
The complicated voting process is staggered over the next six weeks across 27 provinces, divided into thirds with run-offs held a week after the first round in each location.
Voters have to pick two individuals and one alliance or party slate – a system that has left many of the 50 million eligible voters puzzled and apparently undecided.
Since the uprising that toppled Mubarak, Egyptians had looked forward to the election but instead there has been disappointment with the military rulers who replaced the old regime, and the legitimacy of the elections has been questioned.
At least 41 demonstrators have been killed and more than 2,000 wounded in protests in the past 10 days. But the markets reacted positively to Egypt’s election and its benchmark index was up by five per cent within minutes of the start of trading today.