Observers predict tension and possibly violence in the weeks leading to the runoff between Mohammed Morsi of the Brotherhood's Freedom and Justice Party and Ahmed Shafiq, a former general and Mubarak's last prime minister, The Guardian reported Saturday.
In the first round, Morsi captured 24.9 percent of the vote to 24.5 percent for Shafiq, the Egypt Independent said.
Hamdeen Sabbahi, a leftist who finished third in the voting, said he planned to file a lawsuit seeking to suspend the June runoff, The Washington Post reported. At a news conference Saturday, Sabbahi alleged there had been voting irregularities and cited a pending legal matter involving Shafiq, the newspaper reported.
Sabbahi and former Arab League head Amr Moussa -- who also failed to qualify for the runoff -- called for an investigation into claims that an estimated 900,000 Egyptian military personnel and police officers were permitted to vote in violation of a ban on voting by security personnel, the Post reported.
Morsi said at a news conference Saturday his campaign was Egypt's best opportunity to advance the revolution.
"We are certain that the runoff will go in the revolution's favor," he said.
At a separate news conference, Shafiq said his campaign "sought to achieve for Egypt a democracy it thirsted for."
"Our visions differed, our methods varied," he said. "That is the nature of democracy."
Some political observers lamented the choices in the runoff, set for June 16 and 17.
"It feels as if the revolution never took place," said George Ishaq, a founder of the left-wing Kifaya Party. "The Brotherhood are despotic and fanatical, and Shafiq is the choice of Mubarak. It is a very bad result. The revolution is not part of this contest."
Hisham Kassem, a publisher who had backed Amr Moussa, the former head of the Arab League who was knocked out, said of the results: "It's a disaster. Shafiq will try to restore the Mubarak regime. And my trust of the Brotherhood is minus zero."
The Brotherhood-dominated Parliament had passed a law preventing the ousted Mubarak's former aides and prime ministers from running for public office. But the judicial Presidential Election Commission declined to enforce the law, casting doubt on its constitutionality.
Analysts say the Brotherhood's political machine is expected to work to get out the vote for Morsi while the army and police are expected to support Shafiq, even though they're supposed to be officially neutral, The Guardian said.
Mostafa Kamel al-Sayed, a political science professor at Cairo University, called the first-round outcome "the worst-case scenario."
"The revolution happened to establish a civil state. The two candidates who won are the furthest from that civil state. Shafiq comes from the military and a civil state cannot be run by a military man. And the Muslim Brotherhood, they are still opposed to considering Egypt a civil state in the sense of a state not ruled by religion."
Turnout in the first round was reported to be about 40 percent.