Interim president Adly Mansour later joined the meeting, after returning from an Arab League summit in Kuwait, the military said.
Before starting the meeting with the Supreme Council of the Armed Forces, Sisi gathered his belongings at his office in the defence ministry, the official newspaper Al-Ahram reported on its website.
The wildly popular field marshal, who is also defence minister, must resign from the army before running for the presidency.
Underscoring the challenges facing him, at least one person was killed today in clashes between pro-Morsi students and police, the health ministry said.
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Sisi is riding on wave of nationalist fervour and demands for a firm leader who can restore stability after more than three years of turmoil following president Hosni Mubarak's overthrow.
But supporters of Morsi will likely escalate protests.