The prisoners include eight who had been sentenced on political charges, while the others are ordinary criminals.
Among those to be freed include Hisham Abd al-Dhahir Abd al-Rahman, a leader of al-Jamaa al-Islamiya (the Islamic group), whose jailed leaders renounced violence and announced a unilateral ceasefire in 1997.
Several of the group's leaders have already been released. The group fought a violent campaign against Egyptian authorities in the early 1990s to overthrow the government.
It was also blamed for the 1997 attack in the southern city of Luxor that killed 58 tourists and four Egyptians.
Hundreds of prisoners have spent 20 years out of their 25-year life sentences with good behavior but were not released because they were considered a threat to society, including convicted armed robbers and drug traffickers.
After being freed, the prisoners are expected to report to police monthly. If they commit another crime, they will serve out the remainder of their first sentence on top of any subsequent prison term.
Human rights groups have criticised Egypt for detaining political prisoners under emergency legislation that has been in place almost continuously since 1958.