Egyptian flag (Karim Rezk/Creative Commons)

The Guardian reported that with 90 percent of the votes counted, the Brotherhood's Mohammed Morsi scored a plurality with around 26 percent of the vote. Former prime minister Ahmed Shafiq was in position to take the second runoff spot with 23 percent.

Some in Egypt have described the upcoming runoff set for June 16-17 as a "nightmare scenario" for supporters of the revolution, which led to the ouster of President Hosni Mubarak.

"It feels as if the revolution never took place," said George Ishaq, a founder of the leftwing 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."

Shafiq, who positioned himself as the "anti-revolution" candidate in the presidential election, has some worried that he will preserve the Mubarak-style autocracy that had dominated Egyptian politics for years, according to the Associated Press.

Although some Egyptians see Shafiq as a holdover of the Mubarak regime, Morsi's strict Islamist views has others concerned. Morsi, representing the Brotherhood's Freedom and Justice Party, has argued for barring women from the Egyptian presidency and called Israeli leaders "vampires" and "killers," CNN reported.

"A vote for Mohamed Morsi will consolidate the Brotherhood's political influence, which could translate into a constitution with weaker provision for protection of minority and women's rights," Isobel Coleman of the Council on Foreign Relations wrote in a column for CNN.com.

A Brotherhood election win could seal its political stranglehold in Egypt after decades of repression under Mubarak. It currently holds half of parliament after election victories late last year, the AP reported.

The winner of Egypt's runoff election is set to be announced June 21.

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