Egyptian President Abdel Fattah al-Sisi has won a second, four-year term with more than 97 percent of the vote in last week's essentially uncontested election, with a turnout of just 41.5 percent, the election committee said.
The White House said Trump and the Egyptian president spoke by phone after the Egyptian won 97 percent of the vote against a man who was, until recently, his campaign manager.
The State Department said that the U.S. "values its strong partnership with Egypt", but that the White House "noted reports of constraints on freedom of expression and association in the run-up to the elections".
Sisi ran virtually unchallenged after the other serious candidates were arrested or pulled out.
NEA Chairman Lashin Ibrahim announced in a press conference that participation among Egypt's almost 60 million eligible voters, both in the country and overseas, reached 41.05 percent (24,254,152 voters), compared to the 47.45 percent in the 2014 election, in which Sisi came to power for the first time.
State media portrayed failure to vote as a betrayal of Egypt.
Sisi won a total of 21.8 million votes compared with 656,534 for his opponent, Moussa Mostafa Moussa, whose tally was less than the 1.8 million spoiled ballots.
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Last month, Trump came under intense criticism from lawmakers after saying he congratulated Putin on his win at the polls.
"These are momentous moments for this nation...which will be written in letters of light, under the title: battle for the love of Egypt", Ibrahim said as he announced the results.
Sisi first took office after toppling Egypt's first freely elected president, the Muslim Brotherhood's Mohamed Mursi, in a coup d'état in 2013.
The turnout stood at 24,254,152 voters, representing 41 percent of 50,078,138 registered voters.
The vote was held March 26-28 for Egyptians inside the country and March 16-18 for Egyptians overseas.
The election has revealed "obvious problems related to participation and the reluctance of young people (to vote)", said a statement from politician Mohamed Anwar Sadat, a candidate who withdrew in January citing intimidation of his supporters.
Morsi's removal in 2013 ushered in a deadly crackdown that killed and jailed hundreds of Islamists.