Ballot counting has already begun, and preliminary results are expected overnight, with ex-army chief Abdel Fattah al-Sisi certain to win an overwhelming majority against leftist rival Hamdeen Sabbahi.
The move to extend polling for a day drew further criticisms of an election already marred by a deadly crackdown on supporters of deposed Islamist leader Mohamed Morsi.
An electoral official said yesterday that turnout was about 37 per cent, well below the 52 per cent of voters who cast their ballots in the 2012 election Morsi won.
Sisi had urged "40, 45 (million) or even more" of Egypt's 53 million eligible voters to turn out to give credibility to an election boycotted by Morsi's Muslim Brotherhood and secular opposition groups.
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After reports of a meagre numbers at polling stations on the first day of voting Monday, Sisi's backers in the state-run media appealed to people to go out and vote.
An electoral official said polling had been extended to "give a chance to the largest possible number of voters to cast their ballots."
"They didn't get enough votes, so they extended polling into a third day," complained filmmaker Mohamed Ali Hagar, who said he would stay away regardless.
"The state is searching for votes," said a front-page headline of Al-Masry Al-Youm, a newspaper that usually backs Sisi.
The extension of polling casts doubt on the vote's credibility, experts said.
It "raises more questions about the independence of the electoral commission, the impartiality of the government, and the integrity of Egypt's electoral process," said Democracy International, a US-based observer mission.
That echoed criticism from Sabbahi, who said yesterday that the extension raises "questions... About the integrity of the process".