The former army general has overseen an unprecedented political crackdown, silencing critics and jailing thousands.
Mr El-Sissi came to power with the military’s ousting of an elected but divisive Islamist president in 2013, amid mass protests against his one-year-rule.
In the capital, Cairo, dozens of protesters gathered on Friday night near Tahrir Square, the epicentre of the 2011 pro-democracy uprising that toppled long-time autocrat Hosni Mubarak.
Demonstrators chanted slogans echoing the Arab Spring uprisings that briefly defied dictatorships across the region.
The protesters were responding to a call by a self-exiled businessman who claimed corruption by the military and government without providing evidence.
In viral social media videos posted over the past weeks, Muhammad Ali alleged his contracting business had witnessed the large-scale misuse of public funds in the building of luxurious hotels, presidential palaces and a tomb for Mr el-Sisi’s mother, who died in 2014.
The allegations came as economic reforms and austerity have squeezed Egypt’s lower and middle-classes badly.
In a rambling speech on Tuesday, Mr El-Sissi angrily dismissed the allegations as “sheer lies”. He portrayed Mr Ali’s videos as an attempt to weaken Egypt and undermine the public’s trust in the military.
He said he would continue building new presidential residences for the good of the country. “I am building a new country,” he said.
The president also warned Egyptians against protesting or repeating the 2011 uprising.
On Friday, security forces speedily dispersed the scattered protests, which came directly after a football game between al-Ahly, Egypt’s biggest team, and their rivals Zamalek.
No casualties were reported. Unauthorised protests are not allowed in Egypt.
There were also small protests in other cities including the Mediterranean city of Alexandria.
Human Rights Watch (HRW) on Saturday urged Egyptian authorities to protect the right to peaceful protest.
“President al-Sissi’s security agencies have time and again used brutal force to crush peaceful protests,” said Michael Page, deputy Middle East and North Africa director at HRW.
“The authorities should recognise that the world is watching and take all necessary steps to avoid a repetition of past atrocities.”