By noon the operations room of the National Council for Human Rights said it had received 161 complaints since voting began, many related to the late opening of polling stations and concern ballots had not been stamped by the Supreme Election Committee, Ahram Online said.
In many areas violations were reported by members of the Muslim Brotherhood's political arm, the Freedom and Justice Party, who campaigned outside polling booths and handed out leaflets in violation of a 48-hour ban, the site said.
While a number of sporadic outbreaks of violence were reported, the situation appeared calm officials told the site.
Polling stations were guarded by army soldiers and riot police, the very forces held by many to be responsible for the nationwide violence, the British newspaper The Guardian reported.
A Facebook page that played a crucial role in rallying opposition to Mubarak called on voters to go to the polls dressed in black "to show their support to the murdered protesters in the recent protests in Tahrir Square and all over Egypt," the Web page indicated.
At least 42 protesters were killed and thousands were injured in clashes with security forces in weekend protests against military rule.
In addition, photographs of what appeared to be pre-marked ballot papers from Alexandria circulated online, raising fears a Mubarak-era practice of ballot-stuffing would continue, The Guardian said.
Many potential voters Monday appeared unaware of where they were supposed to cast their ballots, and some candidates Sunday tried desperately to withdraw their names from contention to protest the ruling Supreme Council of the Armed Forces and its top officer, Field Marshal Mohamed Hussein Tantawi, The Guardian said.
The Muslim Brotherhood's Freedom and Justice Party is widely expected to emerge as the new Parliament's dominant party in a country that for nearly six decades was the paradigmatic secular dictatorship of the Arab world.
The demonstrators argue, though, the new Parliament will have no real power and simply be a democratic cover for the ruling military council.
The council, which took over when Mubarak was ousted as president Feb. 11, insists it will remain in power despite the escalating bloodshed and amid calls from Washington for the generals to give way to a civilian government.
"We will not allow troublemakers to meddle in these elections," Tantawi said hours before the voting was to start.
"We are at a crossroads," he said. "There are only two routes -- the success of elections, leading Egypt toward safety, or facing dangerous hurdles that we in the armed forces, as part of the Egyptian people, will not allow.
"The position of the armed forces will remain as it is -- it will not change in any new constitution."
The new Parliament will write a new Constitution.
Tantawi, who was Mubarak's defense minister and is now Egypt's de facto head of state and commander in chief, has been the central target of anti-military protests, which accuse him of being a Mubarak extension who is even more brutal and repressive than the longtime ruler.
But Tantawi, 76, alleged Sunday "foreign hands" were behind the mounting unrest and claimed Egypt's failure to pull through the turmoil would lead to "extremely grave consequences."
"Hosni Mubarak used to say the same things," activist Maha Maamoun told the British newspaper The Independent.
Voting in the election is required, with eligible voters who don't go to the polls subject to an $84 fine -- a penalty experts told The Guardian would be almost impossible to enforce.
The two-day elections in Cairo and Alexandria will be followed a week later by a runoff. Further votes in other parts of the country are to take place throughout December and January, with results for the lower house expected Jan. 13 and the upper house, March 14.