Abdel Fatah al-Sisi will be Egypt's next head of state after winning more than 90% of the vote in the presidential elections. As few as 3.5% voted for his single opponent, the labour activist Hamdeen Sabahi.

Initial numbers suggested that more than 46% of Egypt's 53 million eligible voters participated – a respectable turnout comparable with previous post-2011 polls, but which could only be achieved after officials announced a last-minute holiday, extended voting to a third day, and threatened non-voters with a large fine. It was also substantially lower than the 80% turnout Sisi had called for in the days before the election.

Yet, statistically, his victory was a strong one – dwarfing the 13 million who voted in 2012 for Mohamed Morsi, the man Sisi ousted from office last summer. Whether from fear or affection, many have demonstrably placed their trust in a strongman who they hope can stabilise Egypt after three years of post-revolutionary unrest.

"With all this chaos, we need a stronger man than Hosni Mubarak," said Adel Mohamed, a 45-year-old street cleaner, who voted for Sisi on Wednesday.

The scale of Sisi's victory came as no surprise after Egypt's top generals, media personalities and business elite united to present the former army chief as the only patriotic choice, and most challengers declined to take part in the election. But the reported 46% turnout raised eyebrows because to some it seemed high. At the end of the second day of voting, Egypt's prime minister admitted the turnout had only exceeded 30% – leaving sceptics wondering how so many more voters could have participated on the third and final day.

But the head of one of Egypt's only homegrown pollsters, Baseera, said the figures seemed plausible in the context of his company's exit polls. "I think it makes sense based on our numbers," said Magued Osman, who is also a statistics professor at Cairo university. Baseera's 220-strong team interviewed more than 12,000 voters over the three days and calculated turnout to be between 42-46%.

Opposition activists said the election was meaningless amid a months-long crackdown on dissent that has stifled Egypt's opposition and frightened all but one man from challenging Sisi.

The Sabahi campaign claimed that dozens of its activists were arrested after challenging alleged violations at polling stations across the country. A spokesperson said one campaigner, Ahmed Hanafy, was arrested after an argument with an army officer and was now subject to a military trial. Another Sabahi activist, Ayman Zakaria, circulated an image of his beaten torso – said to be the result of a police assault. Asked for comment, an official at Egypt's interior ministry said he needed time to formulate a response.

Mona Selim, a senior organiser at the Sabahi campaign, said: "Police have arrested many members of our campaign. When we say there's something wrong with the election process, instead of writing a record of this problem, they arrest them."

Ahmed Abdeen, another Sabahi campaigner, argued that the police "want to punish [Sabahi] for being the revolution's candidate because they stand with the army's man, Abdel Fatah al-Sisi, and because they want revenge on the revolution."

The validity of the election was also strongly questioned by one of the poll's main international observers. Democracy International (DI) said the decision to extend the election into a third day – in what Sisi's opponents saw as an attempt to raise the turnout to give his victory more credibility – was "just the latest in a series of unusual steps that have seriously harmed the credibility of the process".

It also "raises more questions about the independence of the election commission, the impartiality of the government, and the integrity of Egypt's electoral process," DI added in a statement.

The efforts the state took to encourage people to vote suggests Sisi's popularity is not as universal as his supporters maintain. A small boycott by Morsi's Muslim Brotherhood and secular activists may have dented turnout – as has widespread apathy from voters bored by Egypt's seventh election since the 2011 uprising that ended Mubarak's 30 years in power.

"People don't feel any elections have made any difference," said Ahmed Hassan, 27, a dentist who declared he had not bothered to vote. "I'm not boycotting – I just don't care. There's no point. They've proved that our involvement is not important."