Violence erupted last month as Egyptians marked the second anniversary of the revolution that unseated President Hosni Mubarak after 30 years in power.
Morsi, elected in June, faced a backlash in late January when he declared a state of emergency for parts of the country. That move gave the military certain judicial powers.
A presidential source revealed to Egyptian news agency al-Ahram that Morsi met with members of the Supreme Council of the Armed Forces to discuss security challenges in Egypt.
The meeting was convened late Monday at the Ministry of Defense. SCAF generals were said to update Morsi on internal and external security challenges.
SCAF took power after Mubarak resigned in early 2011. Amnesty International published reports in October that highlight alleged unlawful killings, torture and other abuses at the hands of the military and police during SCAF's tenure.
The reports alleged that police abuse has been "endemic" since the 2011 revolution.