Abdel Fattah al-Sisi. Photo: Reuters

Egyptian President Abdel Fattah al-Sisi has won a second term with 96.9 per cent of valid votes, state media reported on Friday, raising a previous tally from the preliminary count.

The flagship state-owned newspaper Al-Ahram also raised its estimate of turnout in the March 26-28 election to 42.08 per cent, saying 25 million of Egypt´s 60 million registered voters had cast ballots.

On Tuesday, the paper had reported that Sisi was reelected with 92 per cent of the vote on a turnout of just over 40 per cent.

It gave no explanation for the upward revisions.

Sisi, who as army chief ousted Egypt´s first freely elected president -- Mohamed Morsi -- after mass street protests in 2013, won his first term in 2014 with 96.9 per cent of the vote.

The only other candidate on the ballot paper this year, Moussa Mostafa Moussa, won 3.1 per cent of the vote, Al-Ahram said.

Moussa, a little-known politician who is himself a supporter of the president, registered immediately before the close date for applications, saving the election from being a one-horse race.

The National Election Authority is scheduled to announce the full official result on Monday.

Moussa conceded defeat on Wednesday evening, saying he had hoped for 10 per cent of the vote but knew all along that he was up against the "immense popularity" of the president.

More heavyweight would-be challengers were all sidelined, detained or pulled out.

Opposition groups had called for a boycott of this week´s vote which they labelled a charade.

Even at 42 per cent, turnout was down on the 47 per cent in the 2014 election despite appeals from Prime Minister Sherif Ismail for voters to fulfil their patriotic duty.