A decree published on the presidency’s official Facebook page announced the amnesty for deeds “committed with the aim of supporting the revolution and bringing about its objectives, in the period January 25, 2011 to June 30, 2012, with the exception of crimes of first-degree murder.”
Massive protests that erupted on January 25 last year forced Mubarak to stand down after more than 30 years of iron-fisted rule.
The amnesty declaration covers people who already have convictions and those who are still under investigation or are on trial, according to the decree.
It comes 100 days after Morsi, who emerged from the Muslim Brotherhood, became the first freely elected president of Egypt and its first civilian head of state when he took office in June.
The decree was issued on the eve of the first anniversary of the Maspero massacre of 20 protesters during a Coptic Christian demonstration after the torching of church.
Activists have said that thousands of civilians ended up in army courts in the security vacuum that followed the fall of Mubarak in 2011. The campaign group No to Military Trials had said at least 5,000 political prisoners were still in jail.
Many of those jailed were arrested in the protests that erupted during the 18 months an interim military government was in charge in Egypt under the leadership of Field Marshal Hussein Tantawi. Some prisoners have even been tried since Morsi took office in June.