At a press conference in Cairo on Monday, the NEA said 24,254,152 citizens voted in the elections at home and overseas out of more than 59 million eligible voters, representing a turnout of 41.5 percent, according to Al Ahram.
Sisi had always been virtually guaranteed victory after all serious opposition pulled out of the contest earlier this year.
He said 92.73% of the votes were valid from the roughly 24 million cast, while nearly two million ballots were spoilt.
"The sight of Egyptian citizens from all walks of society lining up was impressive and inspiring", Sisi said in a speech to the nation.
Turnout in the 2014 vote that won him his first term was 47 per cent.
He thanked people "who crowded the polling stations" and vowed to work to "increase the common ground" between Egyptians, without differentiating between those who voted for him and those who did not.
Sisi's serious contenders had withdrawn, been sidelined or detained. The flagship state-owned newspaper Al-Ahram also raised its estimate of turnout in the March 26-28 election to 42.08 percent, saying 25 million of Egypt's 60 million registered voters had cast ballots.
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The vote was held March 26-28 for Egyptians inside the country and March 16-18 for Egyptians overseas.
Enjoying near-unanimous media support, Sisi is seen by many Egyptians as the right man to lead the country after years of political, security and economic turmoil that followed the ouster of leader Hosni Mubarak in 2011.
Mr Sisi swept to victory in an election a year later with 97 per cent of the vote.
The United Nations expressed concern over the crackdown on dissent, including the media, which took place before last week's vote.
'President Trump congratulated President Al Sisi on his reelection, ' the White House said in a statement.
Sisi was elected for a four-year presidential term in 2014.
Sisi's main Western and regional allies have been mostly silent over alleged human rights abuses in Egypt.
Earlier the State Department spokeswoman Heather Nauert said the USA "will continue to work to advance our shared objectives" with Egypt, despite its concerns over political freedom.
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