In a clear nod to the Muslim Brotherhood movement, Al-Sisi said that Egypt is now at war with "the strongest secret organization of the last two centuries."
"That means Egyptians took the most critical decisions in modern history, on June 30 and July 3, 2013," he added, referring to the mass protests against then-President Mohamed Morsi, something that finally led to his overthrow.
Al-Sisi made his Chief of Staff Osama Roshdy the head of the new unit, which will be tasked with tackling terror threats east of the Suez, including within restive areas in the Sinai Peninsula.
Meanwhile, the Muslim Brotherhood has said that they were terrified by the killings in Sinai, and that the army should stop displacing people in the volatile peninsula.
"There is no solution to this situation, except by returning the army to its barracks," the Muslim Brotherhood warned.
The Egyptian government draws direct parallels between the Muslim Brotherhood, the Islamic State group and the al-Qaeda in Sinai Peninsula organization, which Cairo says share the same ideology and undermine the country's security.