This raised doubts about the level of support for the man still forecast to win, former army chief Abdel Fattah al-Sisi.
A low turnout would sound a warning to Sisi that he had failed to achieve the resounding mandate he sought after toppling Egypt's first freely elected president, Islamist Mohamed Mursi, following street protests last year.
A tour of Cairo polling stations on Wednesday suggested authorities would again struggle to get more people to cast their ballots. The same pattern emerged in Egypt's second city, Alexandria, Reuters reporters said.
In a country polarized since a popular uprising toppled Hosni Mubarak in 2011, the low turnout was linked to political apathy, opposition to another military man becoming president, discontent at suppression of freedoms among liberal youth, and calls for a boycott by Islamists.
After months of adulation by the media encouraged by his supporters in government, the security services and business, many Egyptians were shocked when the election failed to produce mass support for Sisi, who had called for a turnout of 40 million, or 80 per cent of the electorate.
The two-day vote was originally due to conclude on Tuesday but was extended until 9 pm Wednesday to allow the "greatest number possible" to vote, state media 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,” said Eric Bjornlund, president of Democracy International, in a statement.
Distancing Sisi from the vote extension, seen by commentators as an embarrassing attempt to attract every last vote from a reluctant electorate, his campaign announced that he had objected to the decision.
Sisi's campaign posted pictures of long lines of voters, some waving Egyptian flags and holding posters of Sisi. "Come out and raise the flag of your country," it said on Facebook.
A 45-year-old Cairo shopkeeper, who gave her name as Samaa, said at a polling station in downtown Cairo she was supporting Sisi. "Our country can now only be handled by a military man, we need order."
But voters were scarce. An army officer reading a newspaper outside the same polling station said: "You want to speak with voters? Do you see any voters? I don't know why they're not coming, maybe they reject politics."
Khaled Dawood, a liberal activist, accused the electoral commission and the government of running a chaotic election.
"The feeling is that the result is known in advance and this kind of festival they were creating for Sisi backfired because people no longer buy into this propaganda.
"People in Mubarak's days did not participate because they knew that their vote wouldn’t make a difference and that is what is happening now," he said.
Despite an official campaign to bring out more voters, Reuters reporters found polling places were thinly attended. Egyptians gave various reasons for the lack of enthusiasm.
The Muslim Brotherhood, believed to have one million members, has rejected the poll, describing it as an extension of the army takeover. The group, loyal to Mursi, was outlawed by the military as a terrorist group and saw around 1,000 members killed in a security crackdown.
"Holding these elections is null and void under the military coup ... It cannot be legitimized by elections or in any other way," said Muslim Brotherhood member Mohamed Abdel Hafeez.
Young secular activists, including those who backed Mursi's ouster, had become disillusioned with Sisi after many were rounded up in the security crackdown that also restricted protests.
"The low turnout is a slap in the face for Sisi. I hope he now sees that he only has the votes of old women and men but not us, the youth, who are the majority in this country," said Mohamed Ahmed, 26-year-old employee in a private firm in Cairo.
Voter turnout may have also been low because some Egyptians who decided Sisi's victory was a foregone conclusion saw no point in casting ballots. Others simply did not want to vote for another military man after Mubarak.
Since he gave a series of television interviews, many Egyptians feel Sisi has not spelled out a clear vision of how he would tackle Egypt's challenges, from widespread poverty to an energy crisis and an Islamist insurgency.
His message that Egyptians must endure more austerity may have fueled voter apathy in a country where one leader from the military after another has failed to improve living standards.
Some Brotherhood supporters felt emboldened to speak out, feeling vindicated by the low turnout.
"Now I can say I am a Mursi supporter," said Ahmed Ali, a 28-year-old Cairo shopkeeper.
Unlike the previous election which brought Mursi to power and was contested by a dozen candidates, Sisi faces only one rival now: the leftist Hamdeen Sabahi, whose campaign rejected the extra day of voting.
The justice ministry said Egyptians who did not vote would be fined, and train fares were waived in an effort to boost the numbers. Local media loyal to the government chided the public for not turning out in large enough numbers, and Muslim and Coptic Christian religious leaders also urged people to vote.
In the Sinai, where Egypt's most dangerous militants are based, gunmen killed an Egyptian soldier, security sources said.
In an eastern district of Cairo, gunmen opened fire at an electricity station in what the electricity ministry called a “terrorist” attack.
Egypt is suffering from almost daily power cuts as the country faces a massive energy crunch.