Preliminary results also suggest that an average of 7 percent of electors have invalidated their votes in the overall election.
The voter turnout in the 2014 presidential polls, which Sisi won by almost 97 percent of votes against leftist politician Hamdeen Sabahi, was about 47.5 percent of some 53.8 million registered voters.
According to state-run daily newspaper al-Ahram, as many as 21.4 million cast vote in favour of the 63-year-old who had secured 96.9 percent of the vote in the presidential election back in 2014.
Sisi was expected to make an easy win on his sole rival, a little-known politician, for a second four-year term.
The vote counting started right after closure of polling centers nationwide at 10 p.m. local time (0800 GMT) on Wednesday. The official results will be announced on April 2.
"But I know the vast popularity of President Sisi", he claimed.
Egypt state media reports the current president has won around 90% of the votes that have been counted so far.
With the election seen by many, including Sisi, as a referendum on his presidency, the focus is on turnout which he has sought to support tough economic reforms and a fight against Islamist militants.
In an interview days ahead of the vote, Sisi said he had wished there were more candidates, denying any role in sidelining them.