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Abdel Fattah el-Sisi, Egypt's former army chief who quit in March to run for president, is expected to easily win, but his campaign had hoped for a large turnout as a decisive show of support.
On Wednesday, there was little sign that the number of voters had picked up, with one polling station in the upscale Zamalek district in Cairo failing to attract a single voter more than an hour after it opened, the AP news agency reported.
Supporters of Egypt's first freely elected president, Mohamed Morsi, who was ousted by Sisi last year, have called for a boycott of the vote and have said they will not recognise its outcome.
The head of the Electoral commission, Abdel Aziz Salman, claimed 37% of Egypt's 53 million eligible voters had taken part in the elections but analysts casted doubt on that figure.
Abdullah al-Arian, an assistant professor of History at Georgetown University, told Al Jazeera that the government figures seemed "inflated" based on reports out of the country.
He added that extension of voting for a third day showed that there was a "sense of panic" setting in among Egypt's leaders, who had tried to portray Sisi's election as a "universal concensus".
Sisi's only rival, Hamdeen Sabahi, slammed the ballot extension, saying it called into question the "integrity of the process".