Human Rights Watch has urged Egypt's newly elected president to end the military trials of civilians to bring the country in line with international law.
Egypt's army generals handed over power to the Muslim Brotherhood's Mohammed Mursi last month.
It is thought that they are likely to keep parts of the state apparatus under their control, limiting the president's influence over the military.
At least 12,000 civilians, including children, have been tried by military courts behind closed doors since the uprising in January last year.
Mr Mursi formed a panel this month, headed by a judge, to investigate cases of civilians convicted by military courts.
The committee said 2,165 civilians remained imprisoned after being sentenced and it recommended that they be pardoned by the president.
The report said a presidential pardon was the only way an unfair decision by a military court could be overturned.
Elsewhere, protesters threw tomatoes and shoes at US Secretary of State Hillary Clinton's motorcade during her recent visit.
A tomato struck an Egyptian official in the face, and shoes and a water bottle landed near the armoured cars.
A senior US official said neither Mrs Clinton nor her vehicle, which was around the corner from the incident, were hit.
Protesters chanted "Monica, Monica," a reference to the extra-marital affair conducted by Mrs Clinton's husband, former President Bill Clinton, while in the White House.
