Abdel Fatah al-Sisi was officially confirmed as Egypt's next president on Tuesday evening, after the country's electoral commission announced that he had won 96.1% of last week's presidential runoff.

Officials claimed that just under 47.5% of Egypt's 53 million eligible voters participated – a respectable turnout that, if true, would compare favourably with the 52% who voted in Egypt's 2012 presidential election.

But many of Sisi's critics argued that the figure had been inflated as many polling stations had appeared empty throughout last week's poll, despite non-voters being threatened with a large fine, the introduction of a last-minute public holiday, and the extension of voting to a third day.

Whatever the figure's accuracy, it was substantially lower than the 80% turnout Sisi had called for in the days before the election, and indicated that Sisi's popularity may not be as universal as his allies claim.

His supporters nevertheless made themselves heard on Tuesday evening, with dozens of men invading the stage from which his victory was announced and dancing in their suits. Five miles to the west, thousands of flag-waving wellwishers gathered in Cairo's Tahrir Square to celebrate, in a rally that symbolised the square's transition from a cradle of the 2011 uprising to a parade-ground for the counter-revolution.

His supporters said the field marshal's strong leadership would be the only means of restoring stability to a nation crippled by three years of post-revolutionary economic, political and administrative chaos.

"He will bring back security and will bring the institutions of the country together," said Ayman Iskandar, a 42-year-old silversmith from Sisi's childhood neighbourhood in central Cairo.

State officials sought to portray his victory as the process of a free and fair democratic process, and fiercely rejected suggestions to the contrary. On Saturday, three international observers who lightly criticised the environment in which the election was held were thrown out of an Egyptian-led press conference.

But election observers and opposition activists questioned the validity of an election that took place amid a months-long crackdown on dissent that has stifled Egypt's opposition and frightened all but one man from challenging Sisi.

"Egypt's repressive political environment made a genuinely democratic presidential election impossible," said Eric Bjornlund, president of Democracy International, one of the main international observation missions, in a statement.

Sisi will be sworn in as president on Sunday, in a ceremony to which dozens of foreign heads of state have been invited – including the Iranian president, Hassan Rouhani, according to the Farsi news agency.

If Rouhani attends, it would mark the continuation of a thaw in Egyptian-Iranian relations that began under Mohamed Morsi.