The commission is going to be made up of members of the military and the Interior Ministry as well as a general prosecutor, the country's official Middle East News Agency (MENA) reported on Sunday.
It quoted Morsi as saying "this commission should be formed as soon as possible to release all who were proved not involved in any criminal cases."
A large number of Egyptians were imprisoned, many not formally charged, during last year’s deadly crackdown on protesters calling for the downfall of former dictator Hosni Mubarak’s regime.
Mubarak, his Interior Minister Habib al-Adli, and six police chiefs had been charged with ordering the killing of nearly 900 protesters during the revolution that ousted the dictator on February 11, 2011.
Mubarak and al-Adli were sentenced to life in prison last month, while the police chiefs were acquitted.
Morsi, who was officially sworn in as Egypt’s president on Saturday following run-off presidential polls of June 16-17, has called on all Egyptians to unite, saying the revolution will continue.
"I call on you, great people of Egypt...to strengthen our national unity," he said in his first address following his electoral victory, which had been announced on Jun 24, adding that national unity "is the only way out of these difficult times."