In a statement on its website, the Brotherhood flatly denied what it called "false reports being circulated" and urged election officials to promptly investigate what it called "games and plots." It also accused "the rival candidate's supporters (of) paying cash bribes to some voters," among other allegations.

Outside the city, in Giza, Mohammed Gamea cast his ballot for Morsi even as he questioned whether the election was fairly handled.

"I don't believe the Egyptian presidential elections are fair to begin with," he said Sunday morning. "The military council, assisted by the elections committee, tried everything to stall and influence the process, from disqualifying previous candidates before the first round -- not to mention the negative campaigns against Morsi -- while keeping quiet about Shafik."

"But despite all (this), I don't believe that there has been any electoral fraud. The ballots will determine what is next for Egypt."

Some disgruntled voters launched a campaign to invalidate ballots, said Mohamed Ghoneim, the founder of a group that marked "X" on the names of both Morsi and Shafik, thereby nullifying their vote.

Among the boycotters was Mohamed Khamees, who said he lost sight in his left eye from a police beating in Tahrir Square during the early 2011 protests.

"If I give this country for the Brotherhood hands, there is not going to be any more Egypt, it will be destroyed," he told CNN. "And if I give it to someone from the old system, it looks like we did nothing."