Vote counting began Sunday night after polling stations closed across Egypt in a crucial two-day presidential run-off, DPA reported.
The election pit the Muslim Brotherhood's Mohammed Morsi against Ahmed Shafiq, Hosny Mubarak's last premier, in a vote seen as a power struggle between remnants of the ousted regime and rising Islamists.
Electoral officials were shown live on several Egyptian television stations while counting votes in some polling stations.
Official results are due to be announced on Thursday, according to the election commission.
Polling was extended until 10 pm (2000 GMT) on Sunday to accommodate voters discouraged by soaring temperatures in the earlier hours of the day, said the commission. State media reported that the move did attract more voters in the hours before closing time.
Farouk Sultan, the head of the election commission, Sunday told the Egyptian privately broadcaster CBC that authorities had uncovered a plot to cause unrest after the election.
He added that security forces had arrested three people who were allegedly trying to influence voters outside a polling station in eastern Cairo and confiscated a laptop they were using, in which they found a suspicious CD.
"The CD contained very dangerous information, including a plan to incite a second revolution directed at the presidential palace should the person they want not win ... should a non-Islamist win, in other words, should Ahmed Shafiq win," Sultan said.
The election took place two days after Egypt's highest court invalidated the lower house of parliament, where the Muslim Brotherhood and other Islamists controlled more than two-thirds of seats.
The Muslim Brotherhood, which was banned under Mubarak, along with many secular and leftist Egyptians say a victory for Shafiq would be a blow to the revolution that deposed Mubarak and raised hopes of a transition to democracy.
Shafiq, an ex-army general, has vowed to safeguard the revolution and restore security in Egypt if he becomes a president.
The Brotherhood Sunday condemned a decree issued by the ruling military to officially dissolve the lower house of parliament, in line with the court ruling.
The decree allows the military to have legislative powers and control the budget until a new legislature is elected.
"This represents a coup against the entire democratic process and brings us back to square one," the powerful organization said in a statement.
But Sultan, who is also president of the Supreme Constitutional Court that issued the controversial ruling, rejected the Brotherhood's claim that parliament could only be dissolved following a referendum.
"The rulings of the Supreme Constitutional Court have effect and are binding on all state authorities and on everyone else," he said.
The military rulers are to announce on Monday another constitutional decree setting out the powers of the new president, reported the state-run newspaper Al Ahram.
The new decree, to be unveiled at a press conference on Monday, will also define the powers of the ruling Supreme Council of the Armed Forces, according to the paper.
The military, which took over after Mubarak's overthrow in February 2011, previously promised to transfer power to the new president by the end of this month.
It is not clear if this will take place now that the legislature has been dissolved.