Many Egyptians have failed to vote in a presidential election despite official efforts to boost turnout with an extra day of polling, raising doubts about the level of support for the man still forecast to win, former army chief Abdel Fattah el-Sisi.

On Wednesday, state and privately owned media loyal to Sisi put the turnout at between 37 and 46 percent of the electorate of 54 million. In a speech last week, Sisi had called for 40 million votes, or 80 percent of the electorate.

The electoral commission said that over Monday and Tuesday, the scheduled two days of polling, just 37 percent of eligible voters cast ballots - a number well below the nearly 52 percent who voted in the 2012 election that brought Islamist leader Mohamed Morsi to power.

The lower turnout than Sisi had sought will sound a warning that he had failed to rally the level of popular support he hoped for after toppling Morsi, Egypt's first freely elected president, following street protests last year.

Reuters news agency reported on Wednesday that polling stations in the capital city of Cairo and Egypt’s second city of Alexandria showed that the turnout was lower than anticipated with only a trickle of voters casting their ballots.

The two-day vote was originally due to conclude on Tuesday but was extended until 9 pm (1800 GMT) on Wednesday to allow the "greatest number possible" to vote, state media reported.

One polling station in the upscale Zamalek district in Cairo failed to attract a single voter more than an hour after it opened, the AP news agency reported.

"The state searches for a vote," said a front-page headline in privately owned al-Masry al-Youm newspaper.

The Democracy International observer mission said the decision to extend polling raised questions about the integrity of Egypt's electoral process.

"Last-minute decisions about important election procedures, such as a decision to extend polling by an additional day, should be made only in extraordinary circumstances," Eric Bjornlund, president of Democracy International, said in a statement.

Supporters of Morsi have called for a boycott of the vote and have said they will not recognise its outcome.

The Muslim Brotherhood, believed to have one million members, describes the poll as as an extension of the army takeover, Reuters news agency reported. At least 1,000 members were killed in a security crackdown last year.