The President won with about 92 per cent of the vote, according to preliminary results on Thursday.
Official MENA news agency and other state media, namely Ahram and Akhbar el-Youm, have announced al-Sisi victor of the three-day presidential poll which ended Wednesday.
The three-day election concluded on Wednesday.
According to Al-Ahram, in addition to the 23 million who cast valid votes, two million destroyed their ballot papers.
President Sisi is being criticized for not letting other opponents run in the presidential election except for Mousa Mostafa Mousa.The Media in Egypt accuse that Mousa Mostafa Mousa is running as a supporting candidate.
The vote counting started right after closure of polling centers nationwide at 10 p.m. local time (0800 GMT) on Wednesday.
Even at 42 percent, turnout was down on the 47 percent in the 2014 election despite appeals from Prime Minister Sherif Ismail for voters to fulfil their patriotic duty.
Moussa said he would seek to meet Sisi to present his electoral program, and to submit all the economic files contained in the program for the President.
Boycotters who cannot show good reason for not going to the polls could a face a fine of up to 500 Egyptian pounds (22 euros), the electoral commission has warned.
The opposition is not likely to accept Moussa's leadership, having called for a boycott of these elections that they called a "masquerade".
Moussa, whose presidential ambitions were questioned by many, has repeatedly acknowledged his support for Sisi and his government policies.
The initial crackdown on Morsi's supporters expanded to include liberal and leftist secular activists.